WO2010121140A1 - ANTI-TNF-α ANTIBODIES AND THEIR USES - Google Patents

ANTI-TNF-α ANTIBODIES AND THEIR USES Download PDF

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Publication number
WO2010121140A1
WO2010121140A1 PCT/US2010/031406 US2010031406W WO2010121140A1 WO 2010121140 A1 WO2010121140 A1 WO 2010121140A1 US 2010031406 W US2010031406 W US 2010031406W WO 2010121140 A1 WO2010121140 A1 WO 2010121140A1
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Prior art keywords
tnf
cdr
antibody
binding fragment
seq
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PCT/US2010/031406
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English (en)
French (fr)
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Fiona A. Harding
Yoshiko Akamatsu
Robert B. Dubridge
David B. Powers
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Facet Biotech Corporation
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Priority to JP2012505960A priority Critical patent/JP5795759B2/ja
Priority to SG2011074259A priority patent/SG175181A1/en
Priority to RU2011145428/10A priority patent/RU2595379C2/ru
Priority to EP10719448A priority patent/EP2419448A1/en
Priority to MX2011010908A priority patent/MX2011010908A/es
Priority to CN201080020704.5A priority patent/CN102439040B/zh
Priority to NZ595687A priority patent/NZ595687A/xx
Priority to BRPI1012524-8A priority patent/BRPI1012524A2/pt
Application filed by Facet Biotech Corporation filed Critical Facet Biotech Corporation
Priority to AU2010236256A priority patent/AU2010236256C1/en
Priority to CA2758964A priority patent/CA2758964A1/en
Priority to US13/264,983 priority patent/US20120135005A1/en
Publication of WO2010121140A1 publication Critical patent/WO2010121140A1/en
Priority to IL215649A priority patent/IL215649A/en
Priority to ZA2011/07486A priority patent/ZA201107486B/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/24—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against cytokines, lymphokines or interferons
    • C07K16/241—Tumor Necrosis Factors
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/04—Drugs for disorders of the alimentary tract or the digestive system for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/06—Anti-spasmodics, e.g. drugs for colics, esophagic dyskinesia
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P17/00—Drugs for dermatological disorders
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P19/00—Drugs for skeletal disorders
    • A61P19/02—Drugs for skeletal disorders for joint disorders, e.g. arthritis, arthrosis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P19/00—Drugs for skeletal disorders
    • A61P19/04—Drugs for skeletal disorders for non-specific disorders of the connective tissue
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P3/00—Drugs for disorders of the metabolism
    • A61P3/08—Drugs for disorders of the metabolism for glucose homeostasis
    • A61P3/10—Drugs for disorders of the metabolism for glucose homeostasis for hyperglycaemia, e.g. antidiabetics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/06—Immunosuppressants, e.g. drugs for graft rejection
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value

Definitions

  • the present invention relates to anti-TNF- ⁇ antibodies, pharmaceutical compositions comprising anti-TNF- ⁇ antibodies, and therapeutic uses of such antibodies.
  • Tumor necrosis factor alpha is a pro-inflammatory cytokine that is released by and interacts with cells of the immune system.
  • TNF- ⁇ has been shown to be upregulated in a number of human diseases, including chronic diseases such as rheumatoid arthritis, Crohn's disease, ulcerative colitis and multiple sclerosis.
  • chronic diseases such as rheumatoid arthritis, Crohn's disease, ulcerative colitis and multiple sclerosis.
  • elevated levels of TNF- ⁇ are found in the synovial fluid of rheumatoid arthritis patients and play an important role in both the pathologic inflammation and the joint destruction that are hallmarks of rheumatoid arthritis.
  • TNF- ⁇ is a 17 kDa protein, and the active form exists as a homotrimer (Pennica et al, 1984, Nature 312:724-729; Davis et al, 1987, Biochemistry 26:1322- 1326; Jones et al, 1989, Nature 338:225-228). TNF- ⁇ exerts its biological effects through interaction with two structurally related but functionally distinct cell surface receptors, p55 and p75, that are co-expressed on most cell types (Loetscher et al, 1990, Cell 61 :351-9; Smith et al, 1990, Science 248(4958): 1019-23).
  • p55 is also known as p55R; p55TNFR; CD120a; TNFR I; TNFR 1 and TNFRSFIa.
  • p75 is also known as p75R; p75TNFR; CD120b; TNFR II; TNFR 2 and TNFRSFIb. Both receptors are also proteo lyrically released as soluble molecules capable of binding TNF- ⁇ .
  • Inhibition of TNF- ⁇ activity as a method of treating disease, in particular, rheumatoid arthritis, has been achieved by a number of different means using inhibitors such as antibodies and soluble receptors.
  • Examples include etanercept, marketed by Immunex Corporation as ENB REL® which is a recombinant fusion protein comprising two p75 soluble TNF -receptor domains linked to the Fc portion of a human immunoglobulin.
  • Infliximab marketed by Centocor Corporation as REMICADE®, is a chimeric antibody having murine anti-TNF- ⁇ variable domains and human IgGi constant domains.
  • Other inhibitors include engineered TNF- ⁇ molecules which form trimers with native TNF- ⁇ and prevent receptor binding (Steed et al, 2003, Science 301 :1895-1898; WO 03/033720; WO 01/64889).
  • Adalimumab marketed by Abbott Laboratories as HUMIRA®, is a recombinant, fully human anti-TNF- ⁇ antibody (Tussirot and Wendling, 2004, Expert Opin. Pharmacother. 5:581-594). Adalimumab binds specifically to TNF- ⁇ and blocks its interaction with the p55 and p75 cell surface TNF- ⁇ receptors.
  • Adalimumab also lyses surface TNF- ⁇ expressing cells in vitro via complement-dependent cytotoxicity ("CDC") and antibody-dependent cell-mediated cytotoxicity (“ADCC”). Adalimumab does not bind or inactivate lymphotoxin (TNF- ⁇ ). Adalimumab also modulates biological responses that are induced or regulated by TNF, including changes in the levels of adhesion molecules responsible for leukocyte migration (ELAM-I, VCAM-I, and ICAM-I with an IC 50 of 1-2 X 10 "10 M).
  • Adalimumab can elicit an immune response when administered to humans.
  • Such an immune response can result in an immune complex-mediated clearance of the antibodies or fragments from the circulation and make repeated administration unsuitable for therapy, thereby reducing the therapeutic benefit to the patient and limiting the readministration of the antibody.
  • the present disclosure relates to variants of the anti-TNF- ⁇ antibody D2E7 with improved binding to TNF- ⁇ and/or reduced immunogenicity as compared to D2E7.
  • D2E7 has three heavy chain CDRs, referred to herein (in amino- to carboxy-terminal order) as CDR-Hl (SEQ ID NO:5), CDR-H2 (SEQ ID NO:6), and CDR-H3 (SEQ ID NO:7), and three light chain CDRs, referred to herein (in amino- to carboxy-terminal order) as CDR-Ll (SEQ ID NO:8), CDR-L2 (SEQ ID NO:9), and CDR-L3 (SEQ ID NO: 10).
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments of the disclosure generally have at least one amino acid substitution in at least one CDR as compared to D2E7.
  • At least one amino acid substitution or combination of substitutions is selected from Table 11, Table 12 and/or Table 25. Further mutations (including substitutions, deletions or insertions) can be selected from one or more of Tables 13-25.
  • the present disclosure relates to variants of the anti-TNF- ⁇ antibody D2E7 with improved binding properties, e.g. , improved affinity, to TNF- ⁇ as compared to D2E7.
  • the antibodies of the disclosure have a greater affinity than D2E7 towards TNF- ⁇ , for example improved K D as measured by BIAcore and/or improved affinity as measured by competition ELISA.
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments include at least one substitution selected from S3K in CDR-L2 (SEQ ID NO:9), S3R in CDR-L2 (SEQ ID NO:9), S3N in CDR-L2 (SEQ ID NO:9), T4H in CDR-L2 (SEQ ID NO:9), T4Q in CDR-L2 (SEQ ID NO:9), T4V in CDR-L2 (SEQ ID NO:9), T4F in CDR- L2 (SEQ ID NO:9), T4W in CDR-L2 (SEQ ID NO:9), T4Y in CDR-L2 (SEQ ID NO:9); L5R in CDR-L2 (SEQ ID NO:9), L5K in CDR-L2 (SEQ ID NO:9), Q6K in CDR-L2 (SEQ ID NO:9), Q6R in CDR-L2 (SEQ ID NO:9), D
  • Additional mutations that can be incorporated into the improved affinity variant anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments can be deimmunizing substitutions, such as those described in Table 11, as well as other mutations, e.g., substitutions, that do not destroy the ability of the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments to bind TNF- ⁇ , including but not limited to the known mutations described in Tables 13 to 24 or the mutations described in Table 25.
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments include at least one substitution selected from T4F in CDR-L2, T4W in CDR-L2, T4Y in CDR-L2, L5R in CDR-L2, L5K in CDR-L2, Q6R in CDR-L2, Y2H in CDR-Hl, A3G in CDR-Hl, and T3N in CDR-H2. Additional mutations or combinations of mutations that can be incorporated into such anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments can be selected from one or more of Tables 11 and 13 to 25.
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments include at least one substitution selected from T4F in CDR-L2, T4W in CDR- L2, T4Y in CDR-L2, L5R in CDR-L2, L5K in CDR-L2, Q6R in CDR-L2, Y2H in CDR- Hl, A3 G in CDR-Hl, and T3N in CDR-H2. Additional mutations or combinations of mutations that can be incorporated into such anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments can be selected from one or more of Tables 11 and 13 to 18.
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments include the substitutions G5S + Al 1 S or G5S + Al IG in CDR-Ll . Additional mutations or combinations of mutations that can be incorporated into such anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments can be selected from one or more of Tables 11 to 25.
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments include the substitutions selected from S3N in CDR-L2, T4V in CDR-L2, Q6K in CDR- L2, and DIG in CDR-Hl in combination with at least one substitution selected from Tables 11, 12, and 25. Additional mutations or combinations of mutations that can be incorporated into such anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments can be selected from one or more of Tables 11 to 24.
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments include the substitutions selected from S3N in CDR-L2, T4V in CDR-L2, Q6K in CDR- L2, and DIG in CDR-Hl in combination with at least one substitution selected from S3K in CDR-L2, S3R in CDR-L2, T4H in CDR-L2, T4Q in CDR-L2, T4F in CDR-L2, T4W in CDR-L2, T4Y in CDR-L2, L5R in CDR-L2, L5K in CDR-L2, Q6R in CDR-L2, Y2H in CDR-Hl, A3G in CDR-Hl, and T3N in CDR-H2.
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments include the combination of substitutions selected from at least one of S3K, T4H, L5R and Q6R; S3K, T4Q, L5R and Q6K; S3K, T4Y and L5K; S3K and T4Y; S3N, T4V, L5R and Q6K; S3N, T4W, L5R and Q6R; S3R, T4F and L5R; S3R, T4F, L5R and Q6R; S3R, T4H and Q6K; S3R, T4W, L5K and Q6R; T4H, L5K and Q6K; T4H, L5K and Q6R; T4W, L5R and Q6R; and T4Y and L5R in CDR-L2, wherein the six CDRs altogether have up to 17 amino acid substitutions as compared to CDR sequences of the antibody
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments include one or more substitutions or combinations of substitutions selected from S3K, S3R, S3N, T4F, T4W, T4Y, T4H, T4Q, T4V, L5R, L5K, Q6R, and Q6K in CDR-L2. Additional mutations or combinations of mutations that can be incorporated into such anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments can be selected from one or more of Tables 11 to 24.
  • the present disclosure relates to variants of the anti-TNF- ⁇ antibody D2E7 with reduced immunogenicity as compared to D2E7.
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments include at least one substitution or combination of substitution(s) in CDR-Ll (SEQ ID NO: 8) selected from R7Q; Al IS; R7Q + Al IS; N8T; N8T + Al IS; I6T; Al IG; I6T + Al IG; Q4G; Q4G + A11S; Q4G + A11G; Q4H; Q4H + A11S; Q4R; Q4R + A11S; G5S; G5S + A11S; N8S + Al IS; I6T + Al IS; and N8T + Al IG.
  • Additional mutations that can be incorporated into the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments with reduced antigenicity include substitutions that improve binding properties to TNF- ⁇ , such as those described in Table 12 and/or Table 25, as well as other mutations, e.g., substitutions that do not destroy the ability of the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments to bind TNF- ⁇ , including but not limited to the known mutations described in Tables 13 to 25.
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments of the disclosure have VH and VL sequences having 80% to 99% sequence identity to the VH and VL sequences of D2E7, and include at least one amino acid substitution in at least one CDR as compared to D2E7.
  • the percentage sequence identity for the heavy chain and the light chain compared to the VH and VL sequences of D2E7 is each independently selected from at least 80%, at least 85%, at least 90%, or at least 95% sequence identity.
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments of the disclosure have up to 17 amino acid substitutions in their CDRs as compared to the CDRs of D2E7.
  • Variant antibodies with 17 amino acid substitutions that maintain their target binding capability have been generated by Bostrom et al, 2009, Science 323:1610- 14.
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments of the disclosure can also have up to 16, up to 15, up to 14, up to 13, up to 12, up to 11, up to 10, up to 9, up to 8, up to 7, up to 6, up to 5, or up to 4 amino acid substitutions in their CDRs as compared to CDR sequences of the antibody D2E7.
  • an anti-TNF- ⁇ antibody or anti-TNF- ⁇ binding fragment of the disclosure has, independently:
  • compositions comprising modified anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments having increased affinity to TNF- ⁇ and/or reduced immunogenicity as compared to D2E7.
  • an anti-TNF- ⁇ antibody or anti-TNF- ⁇ binding fragment of the disclosure can be a bispecific antibody or a TNF- ⁇ binding fragment of a bispecif ⁇ c antibody.
  • the bispecific antibody can be specific to TNF- ⁇ and another proinflammatory cytokine (such as, for example, lymphotoxin, interferon- ⁇ , or interleukin-1).
  • Nucleic acids comprising nucleotide sequences encoding the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments of the disclosure are provided herein, as are vectors comprising nucleic acids. Additionally, prokaryotic and eukaryotic host cells transformed with a vector comprising a nucleotide sequence encoding an anti-TNF- ⁇ antibody or anti-TNF- ⁇ binding fragment are provided herein, as well as eukaryotic (such as mammalian) host cells engineered to express the nucleotide sequences. Methods of producing anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments by culturing host cells are also provided.
  • the anti-TNF- ⁇ antibodies and anti-TNF- ⁇ binding fragments of the disclosure are useful in the treatment of immune disorders, e.g., systemic lupus erythematosus, rheumatoid arthritis, thyroidosis, graft versus host disease, scleroderma, diabetes mellitus, Grave's disease, sarcoidosis, chronic inflammatory bowel disease, ulcerative colitis, or Crohn's disease.
  • immune disorders e.g., systemic lupus erythematosus, rheumatoid arthritis, thyroidosis, graft versus host disease, scleroderma, diabetes mellitus, Grave's disease, sarcoidosis, chronic inflammatory bowel disease, ulcerative colitis, or Crohn's disease.
  • Table 1 shows D2E7 VH peptides and D2E7 VL peptides, respectively, that were tested for immunogenicity.
  • Table 2 shows identified CD4+ T cell epitope regions in D2E7. CDR regions are underlined.
  • Table 3 shows HLA class II associations and relative risk of response to the D2E7 VL region peptide epitopes.
  • Table 4 shows sequences of D2E7 VL CDRl epitope variants. A total of 99 donors were tested. The number of responders, the percent of responders, and the average stimulation index is indicated for each peptide tested.
  • Table 5 shows candidate mutations in CDR-Ll for lowering immunogenicity of D2E7.
  • the numbering of the amino acids in Table 5 corresponds to the positions in the context of the D2E7 light chain.
  • Table 6 shows BIAcore and ELISA results for substitutions in CDR-Ll that do not result in significantly decreased binding as compared to D2E7.
  • the numbering of the amino acids in Table 6 corresponds to the positions in the context of the D2E7 light chain. Improvement in K D (as measured by BIAcore) and IC50 of binding (as measured by ELISA) are indicated by "WTx”.
  • CV% refers to the standard deviation as a percentage of the total value measure.
  • Table 7 shows T-cell assay results for all single and double mutations to the D2E7 epitope.
  • Peptide 1 is the parent peptide. Modifications to the parent peptide are in boldfaced type.
  • Table 8 shows the preferred epitope peptide variants based solely on T cell assay results. The numbering of the amino acids in Table 8 corresponds to the positions in the context of the D2E7 light chain.
  • Table 9 shows anti-proliferation bioactivity of antibodies constructed to contain the preferred variant epitope peptides.
  • the parent is unmodified D2E7 antibody.
  • the numbering of the amino acids in Table 9 corresponds to the positions in the context of the D2E7 light chain.
  • Table 10 shows binding kinetics of D2E7 and the D2E7 variants against TNF- ⁇ as analyzed by BIAcore.
  • the numbering of the amino acids in Table 10 corresponds to the positions in the context of the D2E7 light chain.
  • Table 11 shows CDR-Ll substitutions or combinations of substitutions that can be incorporated into D2E7-related antibodies to reduce their immunogenicity.
  • Table 12 shows CDR amino acid substitutions outside CDR-Ll resulting in improved K D (as analyzed by BIAcore), affinity (as measured by ELISA), or both as compared to D2E7.
  • the numbering of the amino acids in Table 12 corresponds to the positions in the context of the D2E7 light and heavy chains. Improvement in K D (as measured by BIAcore) and IC50 of binding (as measured by ELISA) are indicated by "WTx”.
  • CV% refers to the standard deviation as a percentage of the total value measure and "ND" means "not done”.
  • Table 13 shows known mutations in CDR-Hl that can be incorporated into the antibodies of the disclosure.
  • Table 14 shows known mutations in CDR-H2 that can be incorporated into the antibodies of the disclosure.
  • the inclusion of 2 amino acids into a single cell indicates a CDR variant that incorporates an addition to or insertion into the CDR.
  • Shading of a cell indicates a CDR variant that lacks the shaded amino acid residues.
  • Table 15 shows known mutations in CDR-H3 that can be incorporated into the antibodies of the disclosure.
  • Table 16 shows known mutations in CDR-Ll that can be incorporated into the antibodies of the disclosure. The inclusion of 2 amino acids into a single cell indicates a CDR variant that incorporates an addition to or insertion into the CDR.
  • Table 17 shows known mutations in CDR-L2 that can be incorporated into the antibodies of the disclosure. The inclusion of 2 amino acids into a single cell indicates a CDR variant that incorporates the indicated additional N-terminal amino acid into the CDR.
  • Table 18 shows known mutations in CDR-L3 that can be incorporated into the antibodies of the disclosure. The inclusion of 2 amino acids into a single cell indicates a CDR variant that incorporates the indicated additional N-terminal amino acid into the CDR.
  • Table 19 shows further known mutations in CDR-Hl that can be incorporated into the antibodies of the disclosure.
  • Table 20 shows further known mutations in CDR-H2 that can be incorporated into the antibodies of the disclosure.
  • Table 21 shows further known mutations in CDR-H3 that can be incorporated into the antibodies of the disclosure.
  • Table 22 shows further known mutations in CDR-Ll that can be incorporated into the antibodies of the disclosure.
  • Table 23 shows further known mutations in CDR-L2 that can be incorporated into the antibodies of the disclosure.
  • Table 24 shows further known mutations in CDR-L3 that can be incorporated into the antibodies of the disclosure.
  • Table 25 shows combinations of point mutations in CDR-L2 resulting in improved K D (as analyzed by BIAcore), affinity (as measured by ELISA), or both as compared to D2E7.
  • the point mutations can be incorporated singly or in combination into the antibodies of the disclosure.
  • Figures 1A-1E show the amino acid sequences of the D2E7 heavy and light chains, with CDR regions in bold, underlined text.
  • Figure IB shows the CDR sequences and corresponding sequence identifiers of D2E7.
  • Figure 1C shows a correspondence chart between the heavy chain CDR numbering and the heavy chain Kabat numbering.
  • Figure ID shows a correspondence chart between the light chain CDR numbering and the light chain Kabat numbering.
  • Figure IE shows the nucleotide sequences of the heavy and light chain variable regions of D2E7 (SEQ ID NO:1 and SEQ ID NO:3, respectively) as published in U.S. Patent No. 6,090,382.
  • Figure 2 shows percent responses (bottom) and average stimulation indexes (top) to the D2E7 VL peptides.
  • Figure 3 shows average stimulation indexes (top) and percent responses (bottom) to the D2E7 VH peptides.
  • Peptide #27 had an anomalous stimulation index in one donor, and is indicated in darker shading.
  • Figure 4 shows D2E7 VL CDRl epitope peptide variants. Open symbols indicate multiple retests of the unmodified parent peptide within the dataset. Filled symbols represent unique peptide alanine scan variants. The sequence of the most reduced response-inducing variants is indicated.
  • Figure 5 shows D2E7 VL CDRl epitope peptide variants. Open symbols indicate multiple retests of the unmodified parent peptide within the dataset. Filled symbols represent unique peptide variants. The most reduced response-inducing variants are indicated by a circle. This figure graphically represents data from Table 7.
  • Figure 6 shows the results of competition ELISA of D2E7 variant antibodies.
  • ELISA plates were coated with TNF- ⁇ .
  • Biotinylated D2E7 was included in all wells at a single concentration, and the variant antibody was titrated in.
  • the IC50 values were calculated for each antibody. The experiment was performed three times.
  • the Y axis shows average results as a percent of the parent antibody binding.
  • antibody refers to an immunoglobulin molecule that specifically binds to, or is immunologically reactive with, a particular antigen, and includes polyclonal, monoclonal, genetically engineered and otherwise modified forms of antibodies, including but not limited to chimeric antibodies, humanized antibodies, heteroconjugate antibodies (e.g. , bispecif ⁇ c antibodies, diabodies, triabodies, and tetrabodies), and antigen binding fragments of antibodies, including, e.g., Fab', F(ab')2, Fab, Fv, rlgG, and scFv fragments.
  • mAb monoclonal antibody
  • mAb monoclonal antibody
  • Fab and F(ab')2 fragments lack the Fc fragment of intact antibody, clear more rapidly from the circulation of the animal or plant, and may have less non-specific tissue binding than an intact antibody (Wahl et al, 1983, J. Nucl. Med. 24:316).
  • scFv refers to a single chain Fv antibody in which the variable domains of the heavy chain and the light chain from a traditional antibody have been joined to form one chain.
  • references to "VH” refer to the variable region of an immunoglobulin heavy chain of an antibody, including the heavy chain of an Fv, scFv , or Fab.
  • References to “VL” refer to the variable region of an immunoglobulin light chain, including the light chain of an Fv, scFv, dsFv or Fab.
  • Antibodies (Abs) and immunoglobulins (Igs) are glycoproteins having the same structural characteristics. While antibodies exhibit binding specificity to a specific target, immunoglobulins include both antibodies and other antibody-like molecules which lack target specificity.
  • Native antibodies and immunoglobulins are usually heterotetrameric glycoproteins of about 150,000 Daltons, composed of two identical light (L) chains and two identical heavy (H) chains. Each heavy chain has at the amino terminus a variable domain (VH) followed by a number of constant domains. Each light chain has a variable domain at the amino terminus (VL) and a constant domain at the carboxy terminus.
  • the anti-TNF- ⁇ antibodies of the disclosure bind to human TNF- ⁇ and inhibit TNF- ⁇ receptor activity in a cell. Without being bound by any one theory, the inventors believe that the antibodies reduce the binding of TNF- ⁇ to both the low affinity TNF- ⁇ receptor (p75) and the high affinity TNF- ⁇ receptor (p55). [0067]
  • the anti-TNF- ⁇ antibodies of the disclosure contain complementarity determining regions (CDRs) that are related in sequence to the CDRs of the antibody D2E7 (also known as Adalimumab or HUMIRA®).
  • CDRs are also known as hypervariable regions both in the light chain and the heavy chain variable domains.
  • the more highly conserved portions of variable domains are called the framework (FR).
  • FR framework
  • the amino acid position/boundary delineating a hypervariable region of an antibody can vary, depending on the context and the various definitions known in the art.
  • Some positions within a variable domain may be viewed as hybrid hypervariable positions in that these positions can be deemed to be within a hypervariable region under one set of criteria while being deemed to be outside a hypervariable region under a different set of criteria.
  • One or more of these positions can also be found in extended hypervariable regions.
  • the disclosure provides antibodies comprising modifications in these hybrid hypervariable positions.
  • variable domains of native heavy and light chains each comprise four FR regions, largely by adopting a ⁇ - sheet configuration, connected by three CDRs, which form loops connecting (and in some cases forming part of) the ⁇ -sheet structure.
  • the CDRs in each chain are held together in close proximity by the FR regions in the order FRl -CDRl -FR2-CDR2-FR3-CDR3-FR4 and with the CDRs from the other chain, contribute to the formation of the target binding site of antibodies (See Kabat et ah, Sequences of Proteins of Immunological Interest (National Institute of Health, Bethesda, Md. 1987)).
  • numbering of immunoglobulin amino acid residues is done according to the immunoglobulin amino acid residue numbering system of Kabat et al. unless otherwise indicated.
  • sequences of the heavy and light chain variable regions of D2E7 are represented by SEQ ID NO:2 and SEQ ID NO:4, respectively, and encoded by SEQ ID NO.:1 and SEQ ID NO.:3, respectively.
  • the sequences of the heavy and light chain variable regions are also depicted in Figure IA.
  • the sequences of the CDRs of D2E7, and their corresponding identifiers, are presented in Figure IB.
  • the sequences of the heavy and light chain variable regions of D2E7 (as published in U.S. Patent No. 6,090,382) are shown in Figure 1C. Any nucleotide sequences encoding SEQ ID NO:2 or SEQ ID NO:4 can be used in the compositions and methods of the present disclosure.
  • the present disclosure further provides anti-TNF- ⁇ antibody fragments comprising CDR sequences that are related to the CDR sequences of D2E7.
  • antibody fragment refers to a portion of a full-length antibody, generally the target binding or variable region. Examples of antibody fragments include Fab, Fab', F(ab')2 and Fv fragments.
  • An "Fv" fragment is the minimum antibody fragment which contains a complete target recognition and binding site. This region consists of a dimer of one heavy and one light chain variable domain in a tight, noncovalent association (VH-VL dimer). It is in this configuration that the three CDRs of each variable domain interact to define a target binding site on the surface of the VH-VL dimer.
  • Single chain Fv or “scFv” antibody fragments comprise the VH and VL domains of an antibody in a single polypeptide chain.
  • the Fv polypeptide further comprises a polypeptide linker between the VH and VL domain that enables the scFv to form the desired structure for target binding.
  • Single domain antibodies are composed of a single VH or VL domains which exhibit sufficient affinity to the TNF- ⁇ .
  • the single domain antibody is a camelid antibody (see, e.g., Riechmann, 1999, Journal of Immunological Methods 231 :25-38).
  • the Fab fragment contains the constant domain of the light chain and the first constant domain (CHi) of the heavy chain.
  • Fab' fragments differ from Fab fragments by the addition of a few residues at the carboxyl terminus of the heavy chain CHi domain including one or more cysteines from the antibody hinge region.
  • F(ab') fragments are produced by cleavage of the disulfide bond at the hinge cysteines of the F(ab') 2 pepsin digestion product. Additional chemical couplings of antibody fragments are known to those of ordinary skill in the art.
  • the anti-TNF- ⁇ antibodies of the disclosure are monoclonal antibodies.
  • the term "monoclonal antibody” as used herein is not limited to antibodies produced through hybridoma technology.
  • the term “monoclonal antibody” refers to an antibody that is derived from a single clone, including any eukaryotic, prokaryotic, or phage clone and not the method by which it is produced.
  • Monoclonal antibodies useful in connection with the present disclosure can be prepared using a wide variety of techniques known in the art including the use of hybridoma, recombinant, and phage display technologies or a combination thereof.
  • the anti-TNF- ⁇ antibodies of the disclosure include chimeric, primatized, humanized, or human antibodies.
  • the anti-TNF- ⁇ antibodies of the disclosure can be chimeric antibodies.
  • the term "chimeric" antibody as used herein refers to an antibody having variable sequences derived from a non-human immunoglobulin, such as rat or mouse antibody, and human immunoglobulin constant regions, typically chosen from a human immunoglobulin template. Methods for producing chimeric antibodies are known in the art. See, e.g., Morrison, 1985, Science 229(4719): 1202-7; Oi et al, 1986, BioTechniques 4:214-221; Gillies et al, 1985, J. Immunol. Methods 125:191-202; U.S. Pat. Nos. 5,807,715; 4,816,567; and 4,816397, which are incorporated herein by reference in their entireties.
  • the anti-TNF- ⁇ antibodies of the disclosure can be humanized.
  • "Humanized" forms of non-human ⁇ e.g., murine) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab')2 or other target-binding subdomains of antibodies) which contain minimal sequences derived from non-human immunoglobulin.
  • the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin sequence.
  • the humanized antibody can also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin consensus sequence.
  • Fc immunoglobulin constant region
  • Methods of antibody humanization are known in the art. See, e.g., Riechmann et al, 1988, Nature 332:323-7; U.S. Patent Nos: 5,530,101; 5,585,089; 5,693,761; 5,693,762; and 6,180,370 to Queen et al; EP239400; PCT publication WO 91/09967; U.S. Patent No. 5,225,539; EP592106; EP519596; Padlan, 1991, MoI. Immunol, 28:489-498; Studnicka et al, 1994, Prot. Eng.
  • the anti-TNF- ⁇ antibodies of the disclosure can be human antibodies. Completely "human” anti-TNF- ⁇ antibodies can be desirable for therapeutic treatment of human patients.
  • "human antibodies” include antibodies having the amino acid sequence of a human immunoglobulin and include antibodies isolated from human immunoglobulin libraries or from animals transgenic for one or more human immunoglobulin and that do not express endogenous immunoglobulins. Human antibodies can be made by a variety of methods known in the art including phage display methods using antibody libraries derived from human immunoglobulin sequences. See U.S. Patent Nos.
  • Completely human antibodies that recognize a selected epitope can be generated using a technique referred to as "guided selection.”
  • a selected non-human monoclonal antibody e.g., a mouse antibody
  • is used to guide the selection of a completely human antibody recognizing the same epitope Jespers et ⁇ l, 1988, Biotechnology 12:899-903.
  • the anti-TNF- ⁇ antibodies of the disclosure can be primatized.
  • the term "primatized antibody” refers to an antibody comprising monkey variable regions and human constant regions. Methods for producing primatized antibodies are known in the art. See e.g., U.S. Patent Nos. 5,658,570; 5,681,722; and 5,693,780, which are incorporated herein by reference in their entireties.
  • the anti-TNF- ⁇ antibodies of the disclosure can be bispecific antibodies.
  • Bispecific antibodies are monoclonal, often human or humanized, antibodies that have binding specificities for at least two different antigens.
  • one of the binding specificities can be directed towards TNF- ⁇ , the other can be for any other antigen, e.g., for a cell-surface protein, receptor, receptor subunit, tissue-specific antigen, virally derived protein, virally encoded envelope protein, bacterially derived protein, or bacterial surface protein, etc.
  • the anti-TNF- ⁇ antibodies of the disclosure include derivatized antibodies.
  • derivatized antibodies are typically modified by glycosylation, acetylation, pegylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to a cellular ligand or other protein (see Section 7.6 for a discussion of antibody conjugates), etc. Any of numerous chemical modifications can be carried out by known techniques, including, but not limited to, specific chemical cleavage, acetylation, formylation, metabolic synthesis of tunicamycin, etc. Additionally, the derivative can contain one or more non-natural amino acids, e.g., using ambrx technology (See, e.g., Wolfson, 2006, Chem. Biol. 13(10):1011-2).
  • the anti-TNF- ⁇ antibodies or fragments thereof can be antibodies or antibody fragments whose sequence has been modified to alter at least one constant region-mediated biological effector function relative to the corresponding wild type sequence.
  • an anti-TNF- ⁇ antibody of the disclosure can be modified to reduce at least one constant region-mediated biological effector function relative to an unmodified antibody, e.g., reduced binding to the Fc receptor (Fc ⁇ R).
  • Fc ⁇ R binding can be reduced by mutating the immunoglobulin constant region segment of the antibody at particular regions necessary for Fc ⁇ R interactions ⁇ See, e.g., Canfield and Morrison, 1991, J. Exp. Med.
  • Reduction in Fc ⁇ R binding ability of the antibody can also reduce other effector functions which rely on Fc ⁇ R interactions, such as opsonization, phagocytosis and antigen-dependent cellular cytotoxicity ("ADCC").
  • ADCC antigen-dependent cellular cytotoxicity
  • an anti-TNF- ⁇ antibody or fragment thereof can be modified to acquire or improve at least one constant region-mediated biological effector function relative to an unmodified antibody, e.g., to enhance Fc ⁇ R interactions ⁇ See, e.g., US 2006/0134709).
  • an anti-TNF- ⁇ antibody of the disclosure can have a constant region that binds Fc ⁇ RIIA, Fc ⁇ RIIB and/or Fc ⁇ RIIIA with greater affinity than the corresponding wild type constant region.
  • antibodies of the disclosure can have alterations in biological activity that result in increased or decreased opsonization, phagocytosis, or ADCC. Such alterations are known in the art.
  • ADCC lowering variant corresponds to "mutant 3" (shown in Figure 4 of U.S. Patent No. 5,834,597) in which residue 236 is deleted and residues 234, 235 and 237 (using EU numbering) are substituted with alanines.
  • the anti-TNF- ⁇ antibodies of the disclosure have low levels of or lack fucose.
  • Antibodies lacking fucose have been correlated with enhanced ADCC activity, especially at low doses of antibody. See Shields et ah, 2002, J. Biol. Chem. 277:26733-26740; Shinkawa et al, 2003, J. Biol. Chem. 278:3466-73.
  • Methods of preparing fucose-less antibodies include growth in rat myeloma YB2/0 cells (ATCC CRL 1662).
  • YB2/0 cells express low levels of FUT8 mRNA, which encodes ⁇ -1,6- fucosyltransferase, an enzyme necessary for fucosylation of polypeptides.
  • the anti-TNF- ⁇ antibodies or fragments thereof can be antibodies or antibody fragments that have been modified to increase or reduce their binding affinities to the fetal Fc receptor, FcRn, for example, by mutating the immunoglobulin constant region segment at particular regions involved in FcRn interactions (See, e.g., WO 2005/123780).
  • an anti-TNF- ⁇ antibody of the IgG class is mutated such that at least one of amino acid residues 250, 314, and 428 of the heavy chain constant region is substituted alone, or in any combinations thereof, such as at positions 250 and 428, or at positions 250 and 314, or at positions 314 and 428, or at positions 250, 314, and 428, with positions 250 and 428 a specific combination.
  • the substituting amino acid residue can be any amino acid residue other than threonine, including, but not limited to, alanine, cysteine, aspartic acid, glutamic acid, phenylalanine, glycine, histidine, isoleucine, lysine, leucine, methionine, asparagine, proline, glutamine, arginine, serine, valine, tryptophan, or tyrosine.
  • the substituting amino acid residue can be any amino acid residue other than leucine, including, but not limited to, alanine, cysteine, aspartic acid, glutamic acid, phenylalanine, glycine, histidine, isoleucine, lysine, methionine, asparagine, proline, glutamine, arginine, serine, threonine, valine, tryptophan, or tyrosine.
  • the substituting amino acid residues can be any amino acid residue other than methionine, including, but not limited to, alanine, cysteine, aspartic acid, glutamic acid, phenylalanine, glycine, histidine, isoleucine, lysine, leucine, asparagine, proline, glutamine, arginine, serine, threonine, valine, tryptophan, or tyrosine.
  • Specific combinations of suitable amino acid substitutions are identified in Table 1 of U.S. Patent No. 7,217,797, which table is incorporated by reference herein in its entirety. Such mutations increase the antibody's binding to FcRn, which protects the antibody from degradation and increases its half- life.
  • an anti-TNF- ⁇ antibody has one or more amino acids inserted into one or more of its hypervariable regions, for example as described in Jung and Pl ⁇ ckthun, 1997, Protein Engineering 10:9, 959-966; Yazaki et al, 2004, Protein Eng. Des SeI. 17(5):481-9. Epub 2004 Aug 17; and U.S. Pat. App. No. 2007/0280931.
  • the present disclosure encompasses nucleic acid molecules and host cells encoding the anti-TNF- ⁇ antibodies of the disclosure.
  • An anti-TNF- ⁇ antibody of the disclosure can be prepared by recombinant expression of immunoglobulin light and heavy chain genes in a host cell.
  • a host cell is transfected with one or more recombinant expression vectors carrying DNA fragments encoding the immunoglobulin light and heavy chains of the antibody such that the light and heavy chains are expressed in the host cell and, optionally, secreted into the medium in which the host cells are cultured, from which medium the antibodies can be recovered.
  • Standard recombinant DNA methodologies are used to obtain antibody heavy and light chain genes, incorporate these genes into recombinant expression vectors and introduce the vectors into host cells, such as those described in Molecular Cloning; A Laboratory Manual, Second Edition (Sambrook, Fritsch and Maniatis (eds), Cold Spring Harbor, N. Y., 1989), Current Protocols in Molecular Biology (Ausubel, F. M. et al, eds., Greene Publishing Associates, 1989) and in U.S. Patent No. 4,816,397.
  • the anti-TNF- ⁇ antibodies are similar to D2E7 but for changes in one or more framework regions.
  • the anti- TNF- ⁇ antibodies are similar to D2E7 but for changes in one or more CDRs and in one or more framework regions.
  • Germline DNA sequences for human heavy and light chain variable region genes are known in the art (See, e.g., the "VBASE" human germline sequence database; see also Kabat, E. A. et al, 1991, Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242; Tomlinson et al, 1992, J. MoI. Biol. 22T:116-198; and Cox et al, 1994, Eur. J. Immunol.
  • a DNA fragment encoding the heavy or light chain variable region of D2E7 can be synthesized and used as a template for mutagenesis to generate a variant as described herein using routine mutagenesis techniques; alternatively, a DNA fragment encoding the variant can be directly synthesized.
  • DNA fragments encoding D2E7 or D2E7-related VH and VL segments are obtained, these DNA fragments can be further manipulated by standard recombinant DNA techniques, for example, to convert the variable region genes to full-length antibody chain genes, to Fab fragment genes or to a scFv gene.
  • a VL- or VH-encoding DNA fragment is operatively linked to another DNA fragment encoding another protein, such as an antibody constant region or a flexible linker.
  • the term "operatively linked,” as used in this context, is intended to mean that the two DNA fragments are joined such that the amino acid sequences encoded by the two DNA fragments remain in-frame.
  • the isolated DNA encoding the VH region can be converted to a full-length heavy chain gene by operatively linking the VH-encoding DNA to another DNA molecule encoding heavy chain constant regions (CHi, CH 2 , CH 3 and optionally CH 4 ).
  • heavy chain constant regions CHi, CH 2 , CH 3 and optionally CH 4 .
  • the sequences of human heavy chain constant region genes are known in the art (See, e.g., Kabat, E.A. et al, 1991, Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242) and DNA fragments encompassing these regions can be obtained by standard PCR amplification.
  • the heavy chain constant region can be an IgGi, IgG 2 , IgG 3 , IgG 4 , IgA, IgE, IgM or IgD constant region, but in certain embodiments is an IgGi or IgG 4 constant region.
  • the VH-encoding DNA can be operatively linked to another DNA molecule encoding only the heavy chain CHi constant region.
  • the isolated DNA encoding the VL region can be converted to a full-length light chain gene (as well as a Fab light chain gene) by operatively linking the VL-encoding DNA to another DNA molecule encoding the light chain constant region, CL.
  • the sequences of human light chain constant region genes are known in the art (See, e.g., Kabat, E. A. et al, 1991, Sequences of Proteins of Immunological Interest, Fifth Edition (U.S. Department of Health and Human Services, NIH Publication No. 91-3242)) and DNA fragments encompassing these regions can be obtained by standard PCR amplification.
  • the light chain constant region can be a kappa or lambda constant region, but in certain embodiments is a kappa constant region.
  • the VH- and VL-encoding DNA fragments are operatively linked to another fragment encoding a flexible linker, e.g., encoding the amino acid sequence (G ly 4 ⁇ Ser) 3 , such that the VH and VL sequences can be expressed as a contiguous single-chain protein, with the VL and VH regions joined by the flexible linker (See, e.g., Bird et al, 1988, Science 242:423-426; Huston et al, 1988, Proc. Natl. Acad. Sci. USA 85:5879-5883; McCafferty et al, 1990, Nature 348:552-554).
  • a flexible linker e.g., encoding the amino acid sequence (G ly 4 ⁇ Ser) 3
  • DNAs encoding partial or full-length light and heavy chains, obtained as described above, are inserted into expression vectors such that the genes are operatively linked to transcriptional and translational control sequences.
  • operatively linked is intended to mean that an antibody gene is ligated into a vector such that transcriptional and translational control sequences within the vector serve their intended function of regulating the transcription and translation of the antibody gene.
  • the expression vector and expression control sequences are chosen to be compatible with the expression host cell used.
  • the antibody light chain gene and the antibody heavy chain gene can be inserted into separate vectors or, more typically, both genes are inserted into the same expression vector.
  • the antibody genes are inserted into the expression vector by standard methods (e.g. , ligation of complementary restriction sites on the antibody gene fragment and vector, or blunt end ligation if no restriction sites are present).
  • the expression vector Prior to insertion of the D2E7 or D2E7-related light or heavy chain sequences, the expression vector can already carry antibody constant region sequences.
  • one approach to converting the D2E7 or D2E7-related VH and VL sequences to full-length antibody genes is to insert them into expression vectors already encoding heavy chain constant and light chain constant regions, respectively, such that the VH segment is operatively linked to the CH segment(s) within the vector and the VL segment is operatively linked to the CL segment within the vector.
  • the recombinant expression vector can encode a signal peptide that facilitates secretion of the antibody chain from a host cell.
  • the antibody chain gene can be cloned into the vector such that the signal peptide is linked in-frame to the amino terminus of the antibody chain gene.
  • the signal peptide can be an immunoglobulin signal peptide or a heterologous signal peptide (i.e., a signal peptide from a non-immunoglobulin protein).
  • the recombinant expression vectors of the disclosure carry regulatory sequences that control the expression of the antibody chain genes in a host cell.
  • the term "regulatory sequence” is intended to include promoters, enhancers and other expression control elements (e.g., polyadenylation signals) that control the transcription or translation of the antibody chain genes.
  • Such regulatory sequences are described, for example, in Goeddel, Gene Expression Technology: Methods in Enzymology 185 (Academic Press, San Diego, CA, 1990). It will be appreciated by those skilled in the art that the design of the expression vector, including the selection of regulatory sequences may depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc.
  • Suitable regulatory sequences for mammalian host cell expression include viral elements that direct high levels of protein expression in mammalian cells, such as promoters and/or enhancers derived from cytomegalovirus (CMV) (such as the CMV promoter/enhancer), Simian Virus 40 (SV40) (such as the SV40 promoter/enhancer), adenovirus, (e.g., the adenovirus major late promoter (AdMLP)) and polyoma.
  • CMV cytomegalovirus
  • SV40 Simian Virus 40
  • AdMLP adenovirus major late promoter
  • the recombinant expression vectors of the disclosure can carry additional sequences, such as sequences that regulate replication of the vector in host cells (e.g., origins of replication) and selectable marker genes.
  • the selectable marker gene facilitates selection of host cells into which the vector has been introduced (See, e.g., U.S. Patents Nos. 4,399,216, 4,634,665 and 5,179,017, all by Axel et al ).
  • the selectable marker gene confers resistance to drugs, such as G418, puromycin, blasticidin, hygromycin or methotrexate, on a host cell into which the vector has been introduced.
  • Suitable selectable marker genes include the dihydrofolate reductase (DHFR) gene (for use in DHFR " host cells with methotrexate selection/amplification) and the neo gene (for G418 selection).
  • DHFR dihydrofolate reductase
  • neo gene for G418 selection.
  • the expression vector(s) encoding the heavy and light chains is transfected into a host cell by standard techniques.
  • the various forms of the term "transfection” are intended to encompass a wide variety of techniques commonly used for the introduction of exogenous DNA into a prokaryotic or eukaryotic host cell, e.g. , electroporation, lipofection, calcium-phosphate precipitation, DEAE- dextran transfection and the like.
  • eukaryotic cells e.g., mammalian host cells
  • expression of antibodies is performed in eukaryotic cells, e.g., mammalian host cells, for optimal secretion of a properly folded and immunologically active antibody.
  • eukaryotic cells e.g., mammalian host cells
  • Exemplary mammalian host cells for expressing the recombinant antibodies of the disclosure include Chinese Hamster Ovary (CHO cells) (including DHFR " CHO cells, described in Urlaub and Chasin, 1980, Proc. Natl. Acad. Sci. USA 77:4216-4220, used with a DHFR selectable marker, e.g., as described in Kaufman and Sharp, 1982, MoI. Biol.
  • the antibodies are produced by culturing the host cells for a period of time sufficient to allow for expression of the antibody in the host cells or secretion of the antibody into the culture medium in which the host cells are grown. Antibodies can be recovered from the culture medium using standard protein purification methods. Host cells can also be used to produce portions of intact antibodies, such as Fab fragments or scFv molecules. It is understood that variations on the above procedure are within the scope of the present disclosure. For example, it can be desirable to transfect a host cell with DNA encoding either the light chain or the heavy chain (but not both) of an anti-TNF- ⁇ antibody of this disclosure.
  • Recombinant DNA technology can also be used to remove some or all of the DNA encoding either or both of the light and heavy chains that is not necessary for binding to TNF- ⁇ .
  • the molecules expressed from such truncated DNA molecules are also encompassed by the antibodies of the disclosure.
  • bifunctional antibodies can be produced in which one heavy and one light chain are an antibody of the disclosure and the other heavy and light chain are specific for an antigen other than TNF- ⁇ by crosslinking an antibody of the disclosure to a second antibody by standard chemical crosslinking methods.
  • Bifunctional antibodies can also be made by expressing a nucleic acid engineered to encode a bifunctional antibody.
  • dual specific antibodies i.e. antibodies that bind TNF- ⁇ and an unrelated antigen using the same binding site
  • dual specific antibodies can be produced by mutating amino acid residues in the light chain and/or heavy chain CDRs.
  • dual specific antibodies that bind TNF- ⁇ and another antigen for example, another proinflammatory cytokine (such as, for example, lymphotoxin, interferon- ⁇ , or interleukin-1) can be produced by mutating amino acid residues in the periphery of the antigen binding site (See, e.g., Bostrom et al, 2009, Science 323:1610-1614).
  • Dual functional antibodies can be made by expressing a nucleic acid engineered to encode a dual specific antibody.
  • the host cell can be co-transfected with two expression vectors of the disclosure, the first vector encoding a heavy chain derived polypeptide and the second vector encoding a light chain derived polypeptide.
  • the two vectors each contain a separate selectable marker.
  • a single vector can be used which encodes both heavy and light chain polypeptides.
  • nucleic acid encoding one or more portions of D2E7 or of an anti-TNF- ⁇ antibody with CDR sequences related to the CDR sequences of D2E7 is generated, further alterations or mutations can be introduced into the coding sequence, for example to generate nucleic acids encoding antibodies with different CDR sequences, antibodies with reduced affinity to the Fc receptor, or antibodies of different subclasses.
  • the anti-TNF- ⁇ antibodies of the disclosure can also be produced by chemical synthesis (e.g., by the methods described in Solid Phase Peptide Synthesis, 2 nd ed., 1984 The Pierce Chemical Co., Rockford, 111.). Variant antibodies can also be generated using a cell-free platform (see, e.g., Chu et ah, Biochemia No. 2, 2001 (Roche Molecular Biologicals)).
  • an anti-TNF- ⁇ antibody of the disclosure can be purified by any method known in the art for purification of an immunoglobulin molecule, for example, by chromatography (e.g., ion exchange, affinity, particularly by affinity for TNF- ⁇ after Protein A or Protein G selection, and sizing column chromatography), centrifugation, differential solubility, or by any other standard technique for the purification of proteins.
  • chromatography e.g., ion exchange, affinity, particularly by affinity for TNF- ⁇ after Protein A or Protein G selection, and sizing column chromatography
  • centrifugation e.g., centrifugation, differential solubility, or by any other standard technique for the purification of proteins.
  • the anti-TNF- ⁇ antibodies of the present disclosure or fragments thereof can be fused to heterologous polypeptide sequences described herein or otherwise known in the art to facilitate purification.
  • an anti-TNF- ⁇ antibody can, if desired, be further purified, e.g., by high performance liquid chromatography (See, e.g., Fisher, Laboratory Techniques In Biochemistry And Molecular Biology (Work and Burdon, eds., Elsevier, 1980)), or by gel filtration chromatography on a SuperdexTM 75 column (Pharmacia Biotech AB, Uppsala, Sweden).
  • the anti-TNF- ⁇ antibodies of the disclosure have certain biological activities, such as competing with D2E7 for binding to TNF- ⁇ or neutralizing TNF- ⁇ activity.
  • anti-TNF- ⁇ antibodies of the disclosure compete with D2E7 for binding to TNF- ⁇ .
  • the ability to compete for binding to TNF- ⁇ can be tested using a competition assay.
  • TNF- ⁇ is adhered onto a solid surface, e.g., a microwell plate, by contacting the plate with a solution of TNF- ⁇ (e.g., at a concentration of 1 ⁇ g/mL in PBS over night at 4°C). The plate is washed (e.g., 0.1% Tween 20 in PBS) and blocked (e.g., in Superblock, Thermo Scientific, Rockford, IL).
  • ELISA buffer e.g., 1% BSA and 0.1% Tween 20 in PBS
  • the plate is washed, 1 ⁇ g/mL HRP-conjugated Streptavidin diluted in ELISA buffer was added to each well and the plates incubated for 1 hour. Plates are washed and bound antibodies were detected by addition of substrate (e.g., TMB, Biofx Laboratories Inc., Owings Mills, MD). The reaction is terminated by addition of stop buffer (e.g., Bio FX Stop Reagents, Biofx Laboratories Inc., Owings Mills, MD) and the absorbance was measured at 650 nm using microplate reader (e.g., VERSAmax, Molecular Devices, Sunnyvale, CA).
  • substrate e.g., TMB, Biofx Laboratories Inc., Owings Mills, MD
  • stop buffer e.g., Bio FX Stop Reagents, Biofx Laboratories Inc., Owings Mills, MD
  • the absorbance was measured at 650 nm using microplate reader (e.g.,
  • this competition assay can also be used to test competition between an anti- TNF- ⁇ antibody of the disclosure and D2E7.
  • the anti- TNF- ⁇ antibody is used as a reference antibody and D2E7 is used as a test antibody.
  • D2E7 is used as a test antibody.
  • membrane-bound TNF- ⁇ expressed on cell surface for example mammalian cells such as 293S
  • those expressed on cell surface for example mammalian cells such as 293cl8 in culture can be used too.
  • about 10 4 to 10 6 transfectants e.g., about 10 5 transfectants, are used.
  • Other formats for competition assays are known in the art and can be employed.
  • an anti-TNF- ⁇ antibody of the disclosure reduces the binding of labeled D2E7 by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 80%, by at least 90%, or by a percentage ranging between any of the foregoing values (e.g., an anti-TNF- ⁇ antibody of the disclosure reduces the binding of labeled D2E7 by 50% to 70%) when the anti-TNF- ⁇ antibody is used at a concentration of 0.08 ⁇ g/mL, 0.4 ⁇ g/mL, 2 ⁇ g/mL, 10 ⁇ g/mL, 50 ⁇ g/mL, 100 ⁇ g/mL or at a concentration ranging between any of the foregoing values (e.g., at a concentration ranging from 2 ⁇ g/mL to 10 ⁇ g/mL).
  • D2E7 reduces the binding of a labeled anti-TNF- ⁇ antibody of the disclosure by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 80%, by at least 90%, or by a percentage ranging between any of the foregoing values (e.g., D2E7 reduces the binding of a labeled an anti-TNF- ⁇ antibody of the disclosure by 50% to 70%) when D2E7 is used at a concentration of 0.4 ⁇ g/mL, 2 ⁇ g/mL, 10 ⁇ g/mL, 50 ⁇ g/mL, 250 ⁇ g/mL or at a concentration ranging between any of the foregoing values (e.g., at a concentration ranging from 2 ⁇ g/mL to 10 ⁇ g/mL).
  • an anti-TNF- ⁇ antibody of the disclosure inhibits TNF- ⁇ activity in a range of in vitro assays, such as cell cytotoxicity, mitogenesis, cytokine induction, and induction of adhesion molecules.
  • activity of an anti-TNF- ⁇ antibody of the disclosure can be measured by in vitro assays using membrane bound TNF-a naturally or recombinantly expressed on cells, such as ability to induce reverse signaling, cytokine induction, induction of adhesion molecules, CDC and ADCC.
  • An exemplary TNF- ⁇ neutralization assay that measures inhibition of soluble TNF- ⁇ cytotoxicity using cells sensitive to TNF- ⁇ (e.g. , L929) is described below.
  • Other TNF- ⁇ cytotoxicity assays can also be used to assess the activity of the anti-TNF- ⁇ antibodies of the disclosure.
  • an anti-TNF- ⁇ cytotoxicity assays entails plating 3 x 10 4 murine L929 cells into individual wells of a flat bottomed 96-well microtiter plate. The cells are incubated overnight at 37°C in a humidified 5% CO 2 incubator. The next day, serial dilutions of the anti-TNF- ⁇ antibody (e.g., 0.712 ⁇ g/mL, 0.949 ⁇ g/mL, 1.27 ⁇ g/mL, 1.69 ⁇ g/mL, 2.25 ⁇ g/mL or 3 ⁇ g/mL) are prepared in 25 ⁇ L of serum- free medium and added to cells (e.g.
  • final concentration in 150 ⁇ L culture is 119 ng/mL, 158 ng/mL, 211 ng/niL, 282 ng/niL, 375 ng/mL or 500 ng/niL).
  • TNF- ⁇ is added at final concentration of 40 ng/mL (e.g., 25 ⁇ L of 240ng/mL) and the cells were further incubated for 48 hours at 37°C, 5% CO 2 .
  • the wells are scored for cytotoxicity as compared to control plates (which in certain embodiments were treated with TNF- ⁇ that were not incubated with an anti-TNF- ⁇ antibody, e.g., were incubated with an isotype control antibody and in other embodiments were treated with D2E7) using a viability assay (e.g. , CellTiter-Blue, Promega, Madison, WI).
  • a viability assay e.g. , CellTiter-Blue, Promega, Madison, WI.
  • Other formats for TNF- ⁇ neutralization assays are known in the art and can be employed.
  • an anti-TNF- ⁇ antibody of the disclosure neutralizes TNF- ⁇ by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 80%, by at least 90%, or by a percentage ranging between any of the foregoing values (e.g., an anti-TNF- ⁇ antibody of the disclosure neutralizes TNF- ⁇ activity by 50% to 70%) when the anti-TNF- ⁇ antibody is used at a concentration of 2 ng/mL, 5 ng/mL, 10 ng/mL, 20 ng/mL, 0.1 ⁇ g/mL, 0.2 ⁇ g/mL, 1 ⁇ g/mL, 2 ⁇ g/mL, 5 ⁇ g/mL, 10 ⁇ g/mL, 20 ⁇ g/mL, or at a concentration ranging between any of the foregoing values (e.g., at a concentration ranging from 1 ⁇ g/mL to 5 ⁇ g/mL).
  • an anti-TNF- ⁇ antibody of the disclosure is at least 80% as effective, at least 90% as effective, at least 100% as effective, at least 110% as effective, at least 125% as effective or at least 150% as effective, and up to 110% as effective, up to 125% as effective, up to 150% as effective or up to 200% as effective as D2E7 at neutralizing TNF- ⁇ , or any range between any pair of the foregoing values (e.g., 80% to 125% as effective as D2E7 or 125% to 200% as effective as D2E7 in neutralizing TNF- ⁇ ).
  • the anti-TNF- ⁇ antibodies of the disclosure have a high binding affinity for TNF- ⁇ .
  • the anti-TNF- ⁇ antibodies of the present disclosure have specific association rate constants (Ic 0n or k a values), dissociation rate constants (k o ff or kd values), affinity constants (K A values), dissociation constants (K D values) and/or IC 50 values. In certain aspects, such values are selected from the following embodiments.
  • an anti-TNF- ⁇ antibody of the disclosure binds to TNF- ⁇ with a k on of at least 10 5 M -1 S “1 , at least 5 X 10 5 M -1 S “1 , at least 10 6 M -1 S “1 , at least 5 X 10 6 M -1 S “1 , at least 10 7 IVT 1 S “1 , at least 5 X 10 7 at least 10 8 or with a k on of any range between any pair of the foregoing values (e.g., 5 X 10 5 to 5 X 10 6 M -1 S '1 or 10 7 to 10 8 M- 1 S "1 ).
  • an anti-TNF- ⁇ antibody of the disclosure binds to TNF- ⁇ with a koff rate of 5 X 10 "1 s “1 or less, 10 "1 s “1 or less, 5 X 10 "2 s “1 or less, 10 “2 s “1 or less, 5 X 10 "3 s “1 or less, 10 “3 s “1 or less, 5 X 10 “4 s “ V less, 10 "4 s “1 or less, 5 X 10 "5 s “1 or less, 10 "5 s “1 or less, 5 X 10 "6 s “1 or less, 10 “6 s “1 or less, 5 X 10 "7 S -1 Or less, 10 "7 s "1 or less, 5 X 10 "8 s “1 or less, 10 “8 s “1 or less, 5 X 10 "9 s “1 or less, 10 "9 s “1 or less, 5 X 10 "10 s V less, 10 "10
  • an anti-TNF- ⁇ antibody of the disclosure binds to TNF- ⁇ with a K A (k on /k off ) of at least 10 11 nM “1 , at least 5 X 10 11 nM “1 , at least 10 12 nM “1 , at least 5 X 10 12 nM “1 , at least 10 13 nM “1 , at least 5 X 10 13 nM “1 , at least 10 14 nM “1 , at least 5 X 10 14 nM “1 , at least 10 15 nM “1 , at least 5 X 10 15 nM "1 , at least 10 16 nM “1 , at least 5 X 10 16 nM “1 , at least 10 17 nM “1 , at least 5 X 10 17 nM “1 , at least 10 18 nM “1 , at least 5 X 10 18 nM “1 , at least 10 19 nM "1 , at least 10 11 nM "1
  • an anti-TNF- ⁇ antibody of the disclosure binds to TNF- ⁇ with a K D (k off /k on ) of 5 X 10 7 nM or less, 10 7 nM or less, 5 X 10 6 nM or less, 10 6 nM or less, 5 X 10 5 nM or less, 10 5 nM or less, 5 X 10 4 nM or less, 10 4 nM or less, 5 X 10 3 nM or less, 10 3 nM or less, 5 X 10 2 nM or less, 100 nM or less, 90 nM or less, 80 nM or less, 70 nM or less, 60 nM or less, 50 nM or less, 20 nM or less, 15 nM or less, 10 nM or less, 5 nM or less, 3.8 nM or less, 2 nM or less, 1.5 nM or less, 1 nM or less, 5 X 10 "1
  • an TNF- ⁇ antibody of the disclosure binds to TNF- ⁇ with a K D (k o ff/k on ) between approximately 0.1 nM and approximately 1 nM, or approximately 0.1 nM and approximately 2 nM, or approximately 0.1 nM and approximately 3 nM, or approximately 0.1 nM and approximately 4 nM, or approximately 0.1 nM and approximately 5 nM, or approximately 0.1 nM and approximately 6 nM, or approximately 0.1 nM and approximately 7 nM, or approximately 0.1 nM and approximately 8 nM, or approximately 0.1 nM and approximately 9 nM, or approximately 0.1 nM and approximately 10 nM, or between approximately 0.01 nM and approximately 0.1 nM, or between approximately 0.01 nM and approximately 1 nM, or between approximately 0.0 InM and approximately 2 nM, or between approximately 0.01 nM and approximately 3 nM, or between approximately 0.01 nM and approximately 4
  • an anti-TNF- ⁇ antibody binds to TNF- ⁇ with a K D (k off /k on ) of about 5 nM, about 3.5 nM, about 1.5 nM, about 1 nM, about 0.5 nM, about 0.1 nM, about 0.05 nM or about 0.01 nM.
  • the K D (k o ff/k on ) value is determined by assays well known in the art or described herein, e.g., ELISA, isothermal titration calorimetry (ITC), BIAcore, or fluorescent polarization assay.
  • an anti-TNF- ⁇ antibody of the disclosure binds to TNF- ⁇ and inhibits the binding of TNF- ⁇ to p55, p75 or both at an IC50 value of less than 5 X 10 7 nM, less than 10 7 nM, less than 5 X 10 6 nM, less than 10 6 nM, less than 5 X 10 5 nM, less than 10 5 nM, less than 5 X 10 4 nM, less than 10 4 nM, less than 5 X 10 3 nM, less than 10 3 nM, less than 5 X 10 2 nM, less than 100 nM, less than 90 nM, less than 80 nM, less than 70 nM, 65 nM, less than 60 nM, less than 50 nM, less than 40 nM, less than 30 nM, less than 25 nM, less than 20 nM, less than 15 nM, less than 12 nM, less than 10 n
  • an anti-TNF- ⁇ antibody of the disclosure binds to TNF- ⁇ and neutralizes TNF- ⁇ at an IC 50 value of less than 5 X 10 7 nM, less than 10 7 nM, less than 5 X 10 6 nM, less than 10 6 nM, less than 5 X 10 5 nM, less than 10 5 nM, less than 5 X 10 4 nM, less than 10 4 nM, less than 5 X 10 3 nM, less than 10 3 nM, less than 5 X 10 2 nM, less than 100 nM, less than 90 nM, less than 80 nM, less than 70 nM, 65 nM, less than 60 nM, less than 50 nM, less than 40 nM, less than 30 nM, less than 25 nM, less than 20 nM, less than 15 nM, less than 12 nM, less than 10 nM, less than 5 nM, less than 1
  • an anti-TNF- ⁇ antibody binds to TNF- ⁇ and inhibits the binding of TNF- ⁇ to p55, p75 or both, or inhibits TNF- ⁇ activity in a TNF- ⁇ neutralization assay, at an IC50 value of between approximately 1 nM and approximately 10 nM, between approximately 1 nM and approximately 15 nM, between approximately 1 nM and approximately 20 nM, between approximately 1 nM and approximately 25 nM, between approximately 1 nM and approximately 30 nM, between approximately 1 nM and approximately 40 nM, between approximately 1 nM and approximately 50 nM, between approximately 10 nM and approximately 10 2 nM, between approximately 10 2 nM and approximately 10 3 nM, between approximately 10 nM and approximately 10 4 nM, between approximately 10 4 nM and approximately 10 5 nM, between approximately 10 5 nM and approximately 10 6 nM, or between approximately 10 6 nM and approximately 10 7 nM.
  • an anti-TNF- ⁇ antibody binds to TNF- ⁇ and inhibits the binding of TNF- ⁇ to p55, p75 or both, or inhibits TNF- ⁇ activity in a TNF- ⁇ neutralization assay, at an IC50 value of between approximately 5 nM and approximately 10 nM, between approximately 5 nM and approximately 15 nM, between approximately 10 nM and approximately 15 nM, between approximately 10 nM and approximately 20 nM, between approximately 10 nM and approximately 30 nM, between approximately 10 nM and approximately 40 nM, between approximately 10 nM and approximately 50 nM, between approximately 1 nM and approximately 100 nM, between approximately 10 nM and approximately 100 nM, between approximately 20 nM and approximately 100 nM, between approximately 30 nM and approximately 100 nM, between approximately 40 nM and approximately 100 nM, between approximately 50 nM and approximately 100 nM, between approximately 15 nM and approximately 25 nM
  • the IC50 is measured in the presence of TNF- ⁇ at a concentration of 0.001 ⁇ M, 0.005 ⁇ M, 0.01 ⁇ M, 0.05 ⁇ M, 0.1 ⁇ M, 0.5 ⁇ M, 1 ⁇ M, 10 ⁇ M, 20 ⁇ M, 30 ⁇ M, 40 ⁇ M, 50 ⁇ M, 60 ⁇ M, 70 ⁇ M, 80 ⁇ M, 90 ⁇ M, 100 ⁇ M, 200 ⁇ M, 300 ⁇ M, 400 ⁇ M, 500 ⁇ M, 600 ⁇ M, 700 ⁇ M, 800 ⁇ M, 900 ⁇ M, 1000 ⁇ M or at a concentration of any range between any pair of the foregoing values (e.g., 0.01 to 50 ⁇ M, or 10 ⁇ M to 100 ⁇ M).
  • an anti-TNF- ⁇ antibody of the disclosure binds to TNF- ⁇ with a k on rate ranging from 0.2x to 5x of the k on of D2E7, for example a k on of 0.2x of the k on of D2E7, a k on of 0.3x of the k on of D2E7, a k on of 0.4x of the k on of D2E7, a k on of 0.5x of the k on of D2E7, a k on of 0.6x of the k on of D2E7, a k on of 0.7x of the k on of D2E7, a k on of 0.8x of the k on of D2E7, a k on of 0.9x of the k on of D2E7
  • an anti-TNF- ⁇ antibody of the disclosure binds to TNF- ⁇ with a k off rate ranging from 0.2x to 5x of the k off of D2E7, for example a k off of 0.2x of the k off ofD2E7, a koff of 0.3x of the k off of D2E7, a k off of 0.4x of the k off ofD2E7, a k off of 0.5x of the koff of D2E7, a k off of 0.6x of the k off of D2E7, a k off of 0.7x of the k off of D2E7, a k 0 ff of 0.8x of the k o ff of D2E7, a k o ff of 0.9x of the k o ff of D2E7, a k o ff of Ix of the k o ff of D2E7, a
  • an anti-TNF- ⁇ antibody ofthe disclosure binds to TNF- ⁇ with a K A (k on /k off ) ranging from 0.04x to 25x ofthe K A of D2E7, for example a K A of 0.04x ofthe K A of D2E7, a K A of O.lx ofthe K A of D2E7, a K A of 0.25x ofthe K A of D2E7, a K A of 0.5x ofthe K A of D2E7, a K A of 0.6x ofthe K A of D2E7, a K A of 0.7x of the K A of D2E7, a K A of 0.8x ofthe K A of D2E7, a K A of 0.9x ofthe K A of D2E7, a K A of Ix ofthe K A of D2E7, a K A of l.lx ofthe K A of D2E7, a K A of 1.25x ofthe K A of D2E7,
  • an anti-TNF- ⁇ antibody ofthe disclosure binds to TNF- ⁇ a K D (koff/kon) ranging from ranging from 0.04x to 25x ofthe K D of D2E7, for example a K D of 0.04X ofthe K D of D2E7, a K D of O.lx ofthe K D of D2E7, a K D of 0.25x ofthe K D of D2E7, a K D of 0.5x ofthe K D of D2E7, a K D of 0.6x ofthe K D of D2E7, a K D of 0.7x ofthe K D of D2E7, a K D of 0.8x ofthe K D of D2E7, a K D of 0.9x ofthe K D of D2E7, a KD of Ix ofthe K D of D2E7, a K n of l.lx ofthe K D of D2E7, a K D of 1.25x ofthe
  • an anti-TNF- ⁇ antibody of the disclosure binds to TNF- ⁇ and inhibits the binding of TNF- ⁇ to p55, p75 or both at an IC50 value ranging from 50% to 200% of the IC 50 of D2E7, for example an IC 50 of 50% of the IC 50 of D2E7, an IC 50 of 60% of the IC 50 of D2E7, an IC 50 of 70% of the IC 50 of D2E7, an IC 50 of 75% of the IC 50 of D2E7, an IC 50 of 80% of the IC 50 of D2E7, an IC 50 of 90% of the IC 50 of D2E7, an IC 50 of 95% of the IC 50 of D2E7, an IC 50 of 100% of the IC 50 of D2E7, an IC 50 of 110% of the IC 50 of D2E7, an IC 50 of 120% of the IC 50 of D2E7, an IC 50 of 12
  • a single CDR substitution can result in the foregoing differences in IC 50 as compared to D2E7, whereas an anti-TNF- ⁇ antibody of the disclosure can comprise such substitution and up to 16 additional substitutions as compared to D2E7.
  • an anti-TNF- ⁇ antibody of the disclosure binds to TNF- ⁇ and neutralizes TNF- ⁇ at an IC50 value ranging from 50% to 200% of the IC 50 of D2E7, for example an IC 50 of 50% of the IC 50 of D2E7, an IC 50 of 60% of the IC 50 of D2E7, an IC 50 of 70% of the IC 50 of D2E7, an IC 50 of 75% of the IC 50 of D2E7, an IC 50 of 80% of the IC 50 of D2E7, an IC 50 of 90% of the IC 50 of D2E7, an IC 50 of 95% of the IC 50 of D2E7, an IC 50 of 100% of the IC 50 of D2E7, an IC 50 of 110% of the IC 50 of D2E7, an IC 50 of 120% of the IC 50 of D2E7, an IC 50 of 125% of the IC 50 of D2E7,
  • a single CDR substitution can result in the foregoing differences in IC 50 as compared to D2E7, whereas an anti-TNF- ⁇ antibody of the disclosure can comprise such substitution and up to 16 additional substitutions as compared to D2E7.
  • the present disclosure provides anti-TNF- ⁇ antibodies having reduced immunogenicity as compared to D2E7.
  • the present disclosure also provides anti-TNF- ⁇ antibodies having multiple amino acid substitutions in their CDRs as compared to the CDRs of D2E7, wherein at least one substitution reduces the immunogenicity of the antibody as compared to D2E7.
  • the reduced immunogenicity results from one or more amino acid substitutions that result in eliminating or mitigating one or more T cell epitopes.
  • the anti-TNF- ⁇ antibodies of the disclosure having reduced immunogenicity have comparable or improved biological activity as compared to D2E7, e.g., affinity towards TNF- ⁇ or neutralization of TNF- ⁇ activity.
  • Such properties can be tested, for example, by the methods described in Section 7.3 above.
  • the immunogenicity of an TNF- ⁇ antibody of the disclosure is reduced relative to D2E7 antibody.
  • Such antibodies generally have variant sequences relative to the heavy and/or light chain variable region in regions corresponding to SEQ ID NO:81 and/or SEQ ID NO:82, and/or SEQ ID NO:83.
  • the antibodies will generally have one, two or three amino acid substitutions in one, two or all three sequences corresponding to SEQ ID NO:81, SEQ ID NO: 82, and SEQ ID NO: 83, although up to four or five substitutions one, two or all three regions are contemplated herein.
  • Exemplary CDR-Ll substitutions yielding antibodies with lower immunogenicity as compared to D2E7 are listed in Table 11.
  • Antibodies of the disclosure can comprise any of the substitutions or combinations of substitutions listed in Table 11, and, optionally, one or more additional substitutions, such as the CDR mutations in any of Tables 12-25, singly or in combination.
  • the term "reduced immunogenicity" indicates that the variant sequence as compared to SEQ ID NO:81, SEQ ID NO: 82 or SEQ ID NO: 83 elicits a reduced proliferative response in peripheral blood mononuclear cells as compared to a peptide of SEQ ID NO:81, SEQ ID NO: 82, or SEQ ID NO: 83, respectively.
  • An exemplary proliferation assay that can be used to evaluate the proliferative response is set forth in Section 8 below. The reduced proliferative response can be reflected in terms of the percentage of responders, the stimulation index, or both.
  • the variant sequence results in at least 25% fewer responders, in at least 30% fewer responders, in at least 35% fewer responders, in at least 40% fewer responders, in at least 45% fewer responders, in at least 50% fewer responders, in at least 60% fewer responders, in at least 65% fewer responders, in at least 70% fewer responders, in at least 75% fewer responders, in at least 80% fewer responders, in at least 85% fewer responders, in at least 90% fewer responders, in at least 95% fewer responders, 100% fewer responders, or a reduction in responders in a range between any of the foregoing values, e.g., 25%-75% fewer responders, 50%-90% fewer responders, 60%- 100% fewer responders, 70%-90% fewer responders, or the like.
  • the variant sequence results in a stimulation index that is at least 5% less, at least 10% less, at least 15% less, at least 20% less, at least 25% less, at least 30% less, at least 35% less, or at least 40% less than the stimulation index elicited by a peptide of SEQ ID NO:81, SEQ ID NO:82, or SEQ ID NO;83, respectively, or results in a stimulation index reduced by a range between any of the foregoing values as compared to a peptide of SEQ ID NO:81, SEQ ID NO:82, or SEQ ID NO;83, e.g., 5%- 20% less, 10%-30% less, 25%-35% less, 30%-40% less, or the like.
  • Exemplary embodiments of anti-TNF- ⁇ antibodies with reduced immunogenicity as compared to D2E7 comprise one or more of the CDR substitutions or combinations of substitutions set forth in Table 11.
  • the anti-TNF- ⁇ antibodies of the disclosure include antibody conjugates that are modified, e.g., by the covalent attachment of any type of molecule to the antibody, such that covalent attachment does not interfere with binding to TNF- ⁇ .
  • an anti-TNF- ⁇ antibody of the disclosure can be conjugated to an effector moiety or a label.
  • effector moiety includes, for example, antineoplastic agents, drugs, toxins, biologically active proteins, for example enzymes, other antibody or antibody fragments, synthetic or naturally occurring polymers, nucleic acids (e.g., DNA and RNA), radionuclides, particularly radioiodide, radioisotopes, chelated metals, nanoparticles and reporter groups such as fluorescent compounds or compounds which can be detected by NMR or ESR spectroscopy.
  • anti-TNF- ⁇ antibodies can be conjugated to an effector moiety, such as a cytotoxic agent, a radionuclide or drug moiety to modify a given biological response.
  • the effector moiety can be a protein or polypeptide, such as, for example and without limitation, a toxin (such as abrin, ricin A, Pseudomonas exotoxin, or Diphtheria toxin), a signaling molecule (such as ⁇ -interferon, ⁇ -interferon, nerve growth factor, platelet derived growth factor or tissue plasminogen activator), a thrombotic agent or an anti-angiogenic agent (e.g., angiostatin or endostatin) or a biological response modifier such as a cytokine or growth factor (e.g., interleukin-1 (IL-I), interleukin-2 (IL-2), interleukin-6 (IL-6), granulocyte macrophage colony stimulating factor (GM)
  • the effector moieties can be cytotoxins or cytotoxic agents.
  • cytotoxins and cytotoxic agents include taxol, cytochalasin B, gramicidin D, ethidium bromide, emetine, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicin, doxorubicin, daunorabicin, dihydroxy anthracin dione, mitoxantrone, mithramycin, actinomycin D, 1-dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine, propranolol, and puromycin and analogs or homologs thereof.
  • Effector moieties also include, but are not limited to, antimetabolites (e.g. methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil decarbazine), alkylating agents (e.g., mechlorethamine, thioepa chlorambucil, melphalan, carmustine (BSNU) and lomustine (CCNU), cyclothosphamide, busulfan, dibromomannitol, streptozotocin, mitomycin C5 and cis-dichlorodiamine platinum (II) (DDP) cisplatin), anthracyc lines (e.g., daunorubicin (formerly daunomycin) and doxorubicin), antibiotics (e.g., dactinomycin (formerly actinomycin), bleomycin, mithramycin, anthramycin (AMC), calicheamicins or
  • effector moieties can include radionuclides such as, but not limited to, 111 In and 90 Y, Lu 177 , Bismuth 213 , Californium 252 , Iridium 192 and Tungsten 188 /Rhenium 188 and drugs such as, but not limited to, alkylphosphocholines, topoisomerase I inhibitors, taxoids and suramin.
  • radionuclides such as, but not limited to, 111 In and 90 Y, Lu 177 , Bismuth 213 , Californium 252 , Iridium 192 and Tungsten 188 /Rhenium 188
  • drugs such as, but not limited to, alkylphosphocholines, topoisomerase I inhibitors, taxoids and suramin.
  • the antibody or fragment thereof is fused via a covalent bond (e.g., a peptide bond), through the antibody's N-terminus or the C-terminus or internally, to an amino acid sequence of another protein (or portion thereof; for example, at least a 10, 20 or 50 amino acid portion of the protein).
  • the antibody, or fragment thereof can linked to the other protein at the N-terminus of the constant domain of the antibody.
  • Recombinant DNA procedures can be used to create such fusions, for example as described in WO 86/01533 and EP0392745.
  • the effector molecule can increase half-life in vivo, and/or enhance the delivery of an antibody across an epithelial barrier to the immune system. Examples of suitable effector molecules of this type include polymers, albumin, albumin binding proteins or albumin binding compounds such as those described in WO 2005/117984.
  • an anti-TNF- ⁇ antibody is conjugated to a small molecule toxin.
  • an anti-TNF- ⁇ antibody of the disclosure is conjugated to a dolastatin or a dolostatin peptidic analogs or derivatives, e.g., an auristatin (U.S. Pat. Nos. 5,635,483 and 5,780,588).
  • the dolastatin or auristatin drug moiety may be attached to the antibody through its N (amino) terminus, C (carboxyl) terminus or internally (WO 02/088172).
  • Exemplary auristatin embodiments include the N-terminus linked monomethylauristatin drug moieties DE and DF, as disclosed in U.S. Patent No. 7,498,298, which is hereby incorporated by reference in its entirety (disclosing, e.g., linkers and methods of preparing monomethylvaline compounds such as MMAE and MMAF conjugated to linkers).
  • small molecule toxins include but are not limited to calicheamicin, maytansine (U.S. Pat. No. 5,208,020), trichothene, and CC1065.
  • the antibody is conjugated to one or more maytansine molecules (e.g., about 1 to about 10 maytansine molecules per antibody molecule).
  • Maytansine may, for example, be converted to May-SS-Me which may be reduced to May-SH3 and reacted with an antibody (Chari et al, 1992, Cancer Research 52: 127-131) to generate a maytansinoid-antibody or maytansinoid-Fc fusion conjugate.
  • Structural analogues of calicheamicin that can also be used include but are not limited to Yi 1 , Ys 1 , Ys 1 N-acetyl- ⁇ PSAG, and G 1 1 , (Hinman et al, 1993, Cancer Research 53:3336- 3342; Lode et al, 1998, Cancer Research 58:2925-2928; U.S. Patent No. 5,714,586; U.S. Patent No. 5,712,374; U.S. Patent No. 5,264,586; U.S. Patent No. 5,773,001).
  • Antibodies of the disclosure can also be conjugated to liposomes for targeted delivery (See, e.g., Park et al, 1997, Adv. Pharmacol. 40:399-435; Marty & Schiller, 2004, Methods in Molecular Medicine 109:389-401).
  • antibodies of the present disclosure can be attached to poly(ethyleneglycol) (PEG) moieties.
  • the antibody is an antibody fragment and the PEG moieties can be attached through any available amino acid side-chain or terminal amino acid functional group located in the antibody fragment, for example any free amino, imino, thiol, hydroxyl or carboxyl group.
  • Such amino acids can occur naturally in the antibody fragment or can be engineered into the fragment using recombinant DNA methods. See, for example, U.S. Patent No. 5,219,996. Multiple sites can be used to attach two or more PEG molecules.
  • PEG moieties can be covalently linked through a thiol group of at least one cysteine residue located in the antibody fragment. Where a thiol group is used as the point of attachment, appropriately activated effector moieties (for example, thiol selective derivatives such as maleimides and cysteine derivatives) can be used.
  • an anti-TNF- ⁇ antibody conjugate is a modified Fab' fragment which is PEGylated, i.e., has PEG (poly(ethyleneglycol)) covalently attached thereto, e.g., according to the method disclosed in EP0948544.
  • PEG poly(ethyleneglycol)
  • PEG can be attached to a cysteine in the hinge region.
  • a PEG-modif ⁇ ed Fab' fragment has a maleimide group covalently linked to a single thiol group in a modified hinge region.
  • a lysine residue can be covalently linked to the maleimide group and to each of the amine groups on the lysine residue can be attached a methoxypoly(ethyleneglycol) polymer having a molecular weight of approximately 20,000 Da.
  • the total molecular weight of the PEG attached to the Fab' fragment can therefore be approximately 40,000 Da.
  • label when used herein refers to a detectable compound or composition which can be conjugated directly or indirectly to an anti-TNF- ⁇ antibody of the disclosure.
  • the label can itself be detectable (e.g., radioisotope labels or fluorescent labels) or, in the case of an enzymatic label, can catalyze chemical alteration of a substrate compound or composition which is detectable.
  • Useful fluorescent moieties include, but are not limited to, fluorescein, fluorescein isothiocyanate, rhodamine, 5- dimethylamine-1-napthalenesulfonyl chloride, phycoerythrin and the like.
  • Useful enzymatic labels include, but are not limited to, alkaline phosphatase, horseradish peroxidase, glucose oxidase and the like.
  • anti-TNF- ⁇ antibodies of the disclosure including those antibodies that have been modified, e.g., by biotinylation, horseradish peroxidase, or any other detectable moiety (including those described in Section 7.6), can be advantageously used for diagnostic purposes.
  • the anti-TNF- ⁇ antibodies can be used, for example, but not limited to, to purify or detect TNF- ⁇ , including both in vitro and in vivo diagnostic methods.
  • the antibodies have use in immunoassays for qualitatively and quantitatively measuring levels of TNF- ⁇ in biological samples. See, e.g., Harlow et ah, Antibodies: A Laboratory Manual, Second Edition (Cold Spring Harbor Laboratory Press, 1988), which is incorporated by reference herein in its entirety.
  • the anti-TNF- ⁇ antibodies of the disclosure can be used for detecting and quantitating levels of TNF- ⁇ in the serum.
  • the present disclosure further encompasses antibodies or fragments thereof conjugated to a diagnostic agent.
  • the antibodies can be used diagnostically, for example, to detect expression of a target of interest in specific cells, tissues, or serum; or to monitor the development or progression of an immunologic response as part of a clinical testing procedure to, e.g., determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, radioactive materials, positron emitting metals using various positron emission tomographies, and nonradioactive paramagnetic metal ions.
  • the detectable substance can be coupled or conjugated either directly to the antibody (or fragment thereof) or indirectly, through an intermediate (such as, for example, a linker known in the art) using techniques known in the art.
  • enzymatic labels include luciferases ⁇ e.g., firefly luciferase and bacterial luciferase; U.S. Patent No.
  • luciferin 2,3-dihydrophthalazinediones, malate dehydrogenase, urease, peroxidase such as horseradish peroxidase (HRPO), alkaline phosphatase, ⁇ - galactosidase, acetylcholinesterase, glucoamylase, lysozyme, saccharide oxidases ⁇ e.g., glucose oxidase, galactose oxidase, and glucose-6-phosphate dehydrogenase), heterocyclic oxidases (such as uricase and xanthine oxidase), lactoperoxidase, microperoxidase, and the like.
  • HRPO horseradish peroxidase
  • alkaline phosphatase ⁇ - galactosidase
  • acetylcholinesterase glucoamylase
  • lysozyme saccharide oxidases ⁇ e.g
  • suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin;
  • suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin;
  • an example of a luminescent material includes luminol;
  • examples of bio luminescent materials include luciferase, luciferin, and aequorin; and examples of suitable radioactive material include 125 I, 131 I, 111 In or 99 Tc.
  • the disclosure provides for the detection of expression of TNF- ⁇ , comprising contacting a biological sample (cells, tissue, or body fluid of an individual) using one or more anti-TNF- ⁇ antibodies of the disclosure (optionally conjugated to detectable moiety), and detecting whether or not the sample is positive for TNF- ⁇ expression, or whether the sample has altered (e.g. , reduced or increased) expression as compared to a control sample.
  • tissue or body fluid is peripheral blood, peripheral blood leukocytes, biopsy tissues such as lung or skin biopsies, and tissue.
  • TNF- ⁇ antibodies of the present disclosure are useful for treating disorders or symptoms of various immune and autoimmune pathologies as well as inflammatory diseases.
  • TNF- ⁇ -related pathologies and diseases that can be treated with the anti-TNF- ⁇ antibodies of the disclosure include, but are not limited to, the following:
  • Acute and chronic immune and autoimmune pathologies such as systemic lupus erythematosus, rheumatoid arthritis, thyroidosis, graft versus host disease, scleroderma, diabetes mellitus, Grave's disease, and the like;
  • Infections including, but not limited to, sepsis syndrome, cachexia, circulatory collapse and shock resulting from acute or chronic bacterial infection, acute and chronic parasitic and/or bacterial, viral or fungal infectious diseases, such as AIDS (including sequelae such as cachexia, autoimmune disorders, AIDS dementia complex and infections); • Inflammatory diseases, such as chronic inflammatory pathologies and vascular inflammatory pathologies, including chronic inflammatory pathologies such as sarcoidosis, chronic inflammatory bowel disease, ulcerative colitis, and Crohn's pathology and vascular inflammatory pathologies, such as, but not limited to, disseminated intravascular coagulation, atherosclerosis, and Kawasaki's pathology;
  • AIDS including sequelae such as cachexia, autoimmune disorders, AIDS dementia complex and infections
  • Inflammatory diseases such as chronic inflammatory pathologies and vascular inflammatory pathologies, including chronic inflammatory pathologies such as sarcoidosis, chronic inflammatory bowel disease, ulcerative colitis, and Crohn
  • Neurodegenerative diseases including, but not limited to, demyelinating diseases, such as multiple sclerosis and acute transverse myelitis; extrapyramidal and cerebellar disorders' such as lesions of the corticospinal system; disorders of the basal ganglia or cerebellar disorders; hyperkinetic movement disorders such as Huntington's Chorea and senile chorea, drug-induced movement disorders, such as those induced by drugs which block the CNS, dopamine receptors; hypokinetic movement disorders, such as Parkinson's disease; Progressive supranucleo palsy, Cerebellar and Spinocerebellar Disorders, such as astructural lesions of the cerebellum; spinocerebellar degenerations (spinal ataxia, Friedreich's ataxia, cerebellar cortical degenerations, multiple systems degenerations (Mencel, Dejerine-Thomas, Shi-Drager, and Machado-Joseph); and systemic disorders (Refsum's disease, abetal
  • demyelinating core disorders such as multiple sclerosis, acute transverse myelitis
  • disorders of the motor unit such as neurogenic muscular atrophies (anterior horn cell degeneration, such as amyotrophic lateral sclerosis, infantile spinal muscular atrophy and juvenile spinal muscular atrophy); Alzheimer's disease; Down's Syndrome in middle age; Diffuse Lewy body disease; Senile Dementia of Lewy body type, Wernicke-Korsakoff syndrome; chronic alcoholism; Creutzfeldt- Jakob disease; subacute sclerosing panencephalitis, Hallerrorden-Spatz disease,- and Dementia pugilistica, or any subset thereof;
  • TNF- ⁇ secreting tumors or other malignancies involving TNF- ⁇ such as, but not limited to leukemias (acute, chronic myelocytic, chronic lymphocytic and/or myelodyspastic syndrome); lymphomas (Hodgkin's and non-Hodgkin's lymphomas, such as malignant lymphomas (Burkitt's lymphoma or Mycosis fungoides), and
  • the antibodies of the disclosure are used to treat one or more of:
  • JIA polyarticular juvenile idiopathic arthritis
  • PsA Psoriatic arthritis
  • the present disclosure provides methods of treating any of the foregoing diseases in a patient in need thereof, comprising: administering to the patient an anti-TNF- ⁇ antibody of the disclosure.
  • said administration is repeated, e.g., after one day, two days, three days, five days, one week, two weeks, three weeks, one month, five weeks, six weeks, seven weeks, eight weeks, two months, or three months.
  • the repeated administration can be at the same dose or at a different dose.
  • the administration can be repeated once, twice, three times, four times, five times, six times, seven times, eight times, nine times, ten times, or more.
  • a patient receives anti-TNF- ⁇ therapy for a prolonged period of time, e.g., 6 months, 1 year or more.
  • the amount of anti-TNF- ⁇ antibody administered to the patient is in certain embodiments a therapeutically effective amount.
  • a "therapeutically effective" amount of TNF- ⁇ antibody can be administered as a single dose or over the course of a therapeutic regimen, e.g. , over the course of a week, two weeks, three weeks, one month, three months, six months, one year, or longer. Exemplary therapeutic regimens are described in Section 7.11 below.
  • treatment of a disease encompasses the treatment of patients already diagnosed as having any form of the disease at any clinical stage or manifestation; the delay of the onset or evolution or aggravation or deterioration of the symptoms or signs of the disease; and/or preventing and/or reducing the severity of the disease.
  • a "subject" or “patient” to whom the anti-TNF- ⁇ antibody of the disclosure is administered is preferably a mammal such as a non-primate (e.g., cow, pig, horse, cat, dog, rat, etc.) or a primate (e.g., monkey or human).
  • a non-primate e.g., cow, pig, horse, cat, dog, rat, etc.
  • a primate e.g., monkey or human.
  • the subject or patient is a human.
  • the human is a pediatric patient. In other aspects, the human is an adult patient.
  • compositions comprising an anti-TNF- ⁇ antibody of the disclosure and, optionally one or more additional therapeutic agents, such as the combination therapeutic agents described in Section 7.10 below, are provided herein.
  • the compositions will usually be supplied as part of a sterile, pharmaceutical composition that will normally include a pharmaceutically acceptable carrier. This composition can be in any suitable form (depending upon the desired method of administering it to a patient).
  • the anti-TNF- ⁇ antibodies of the disclosure can be administered to a patient by a variety of routes such as orally, transdermally, subcutaneously, intranasally, intravenously, intramuscularly, intraocularly, topically, intrathecally and intracerebroventricularly.
  • routes such as orally, transdermally, subcutaneously, intranasally, intravenously, intramuscularly, intraocularly, topically, intrathecally and intracerebroventricularly.
  • routes for administration in any given case will depend on the particular antibody, the subject, and the nature and severity of the disease and the physical condition of the subject.
  • the effective dose of an anti-TNF- ⁇ antibody of the disclosure can range from about 0.001 to about 75 mg/kg per single (e.g., bolus) administration, multiple administrations or continuous administration, or to achieve a serum concentration of 0.01-5000 ⁇ g/mL serum concentration per single (e.g., bolus) administration, multiple administrations or continuous administration, or any effective range or value therein depending on the condition being treated, the route of administration and the age, weight and condition of the subject.
  • each dose can range from about 0.5 ⁇ g to about 50 ⁇ g per kilogram of body weight, for example from about 3 ⁇ g to about 30 ⁇ g per kilogram body weight.
  • the antibody can be formulated as an aqueous solution and administered by subcutaneous injection.
  • compositions can be conveniently presented in unit dose forms containing a predetermined amount of an anti-TNF- ⁇ antibody of the disclosure per dose.
  • a unit can contain for example but without limitation 5 mg to 5 g, for example 10 mg to 1 g, or 20 to 50 mg.
  • Pharmaceutically acceptable carriers for use in the disclosure can take a wide variety of forms depending, e.g., on the condition to be treated or route of administration.
  • Therapeutic formulations of the anti-TNF- ⁇ antibodies of the disclosure can be prepared for storage as lyophilized formulations or aqueous solutions by mixing the antibody having the desired degree of purity with optional pharmaceutically-acceptable carriers, excipients or stabilizers typically employed in the art (all of which are referred to herein as "carriers"), i.e., buffering agents, stabilizing agents, preservatives, isotonifiers, non-ionic detergents, antioxidants, and other miscellaneous additives. See, Remington's Pharmaceutical Sciences, 16th edition (Osol, ed. 1980). Such additives must be nontoxic to the recipients at the dosages and concentrations employed.
  • Buffering agents help to maintain the pH in the range which approximates physiological conditions. They can be present at concentration ranging from about 2 mM to about 50 mM.
  • Suitable buffering agents for use with the present disclosure include both organic and inorganic acids and salts thereof such as citrate buffers (e.g.
  • succinate buffers e.g., succinic acid- monosodium succinate mixture, succinic acid-sodium hydroxide mixture, succinic acid- disodium succinate mixture, etc.
  • tartrate buffers e.g., tartaric acid-sodium tartrate mixture, tartaric acid-potassium tartrate mixture, tartaric acid-sodium hydroxide mixture, etc.
  • fumarate buffers e.g., fumaric acid-monosodium fumarate mixture, fumaric acid- disodium fumarate mixture, monosodium fumarate-disodium fumarate mixture, etc.
  • gluconate buffers e.g., gluconic acid-sodium glyconate mixture, gluconic acid-sodium hydroxide mixture, gluconic acid-potassium
  • oxalic acid-sodium oxalate mixture oxalic acid-sodium hydroxide mixture, oxalic acid-potassium oxalate mixture, etc.
  • lactate buffers e.g., lactic acid-sodium lactate mixture, lactic acid-sodium hydroxide mixture, lactic acid-potassium lactate mixture, etc.
  • acetate buffers e.g., acetic acid-sodium acetate mixture, acetic acid-sodium hydroxide mixture, etc.
  • phosphate buffers, histidine buffers and trimethylamine salts such as Tris can be used.
  • Preservatives can be added to retard microbial growth, and can be added in amounts ranging from 0.2%-l% (w/v).
  • Suitable preservatives for use with the present disclosure include phenol, benzyl alcohol, meta-cresol, methyl paraben, propyl paraben, octadecyldimethylbenzyl ammonium chloride, benzalconium halides ⁇ e.g., chloride, bromide, and iodide), hexamethonium chloride, and alkyl parabens such as methyl or propyl paraben, catechol, resorcinol, cyclohexanol, and 3-pentanol.
  • Isotonicif ⁇ ers sometimes known as “stabilizers” can be added to ensure isotonicity of liquid compositions of the present disclosure and include polhydric sugar alcohols, for example trihydric or higher sugar alcohols, such as glycerin, erythritol, arabitol, xylitol, sorbitol and mannitol.
  • Stabilizers refer to a broad category of excipients which can range in function from a bulking agent to an additive which solubilizes the therapeutic agent or helps to prevent denaturation or adherence to the container wall.
  • Typical stabilizers can be polyhydric sugar alcohols (enumerated above); amino acids such as arginine, lysine, glycine, glutamine, asparagine, histidine, alanine, ornithine, L-leucine, 2-phenylalanine, glutamic acid, threonine, etc., organic sugars or sugar alcohols, such as lactose, trehalose, stachyose, mannitol, sorbitol, xylitol, ribitol, myoinisitol, galactitol, glycerol and the like, including cyclitols such as inositol; polyethylene glycol; amino acid polymers; sulfur containing reducing agents, such as urea, glutathione, thioctic acid, sodium thioglycolate, thioglycerol, ⁇ -monothioglycerol and sodium thio sulfate; low
  • Non-ionic surfactants or detergents can be added to help solubilize the therapeutic agent as well as to protect the therapeutic protein against agitation-induced aggregation, which also permits the formulation to be exposed to shear surface stressed without causing denaturation of the protein.
  • Suitable non-ionic surfactants include polysorbates (20, 80, etc.), polyoxamers (184, 188 etc.), Pluronic polyols, polyoxyethylene sorbitan monoethers (TWEEN®-20, TWEEN®-80, etc.).
  • Nonionic surfactants can be present in a range of about 0.05 mg/mL to about 1.0 mg/mL, for example about 0.07 mg/mL to about 0.2 mg/mL.
  • Additional miscellaneous excipients include bulking agents ⁇ e.g., starch), chelating agents ⁇ e.g., EDTA), antioxidants ⁇ e.g., ascorbic acid, methionine, vitamin E), and cosolvents.
  • Further formulations suitable for the anti-TNF- ⁇ antibodies of the disclosure are disclosed in U.S. Pat. App. No. 2004/0033228 Al, the contents of which are incorporated by reference herein in their entirety.
  • the formulation herein can also contain a combination therapeutic agent in addition to the anti-TNF- ⁇ antibody of the disclosure.
  • a combination therapeutic agent in addition to the anti-TNF- ⁇ antibody of the disclosure. Examples of suitable combination therapeutic agents are provided in Section 7.10 below.
  • the dosing schedule for subcutaneous administration can vary from once every six months, five months, four months, three months, two months, once a month to biweekly, weekly, or daily depending on a number of clinical factors, including the type of disease, severity of disease, and the patient's sensitivity to the anti-TNF- ⁇ antibody.
  • an anti-TNF- ⁇ antibody of the disclosure to be administered of will vary according to the particular antibody, the type of autoimmune or inflammatory disease, the subject, and the nature and severity of the disease, the physical condition of the subject, the therapeutic regimen ⁇ e.g., whether a combination therapeutic agent is used), and the selected route of administration; the appropriate dosage can be readily determined by a person skilled in the art.
  • compositions comprising anti-TNF- ⁇ antibodies can be administered to patients ⁇ e.g., human subjects) at therapeutically or prophylactically effective dosages ⁇ e.g., dosages which result in inhibition of an autoimmune or inflammatory disease and/or relief of autoimmune or inflammatory disease symptoms) using any suitable route of administration, such as injection and other routes of administration known in the art for antibody-based clinical products.
  • the combinatorial methods of the disclosure involve the administration of at least two agents to a patient, the first of which is an anti-TNF- ⁇ antibody of the disclosure, and the additional agent(s) is a combination therapeutic agent.
  • the anti-TNF- ⁇ antibody and the combination therapeutic agent(s) can be administered simultaneously, sequentially or separately.
  • combinatorial therapy methods of the present disclosure can result in a greater than additive effect, providing therapeutic benefits where neither the anti-TNF- ⁇ antibody or combination therapeutic agent administered in an amount that is alone therapeutically effective.
  • the anti-TNF- ⁇ antibody of the disclosure and the combination therapeutic agent can be administered concurrently, either simultaneously or successively.
  • the anti-TNF- ⁇ antibody of the disclosure and the combination therapeutic agent are said to be administered successively if they are administered to the patient on the same day, for example during the same patient visit. Successive administration can occur 1, 2, 3, 4, 5, 6, 7 or 8 hours apart.
  • the anti-TNF- ⁇ antibody of the disclosure and the combination therapeutic agent are said to be administered separately if they are administered to the patient on the different days, for example, the anti-TNF- ⁇ antibody of the disclosure and the combination therapeutic agent can be administered at a 1-day, 2-day or 3 -day, one-week, 2-week or monthly intervals.
  • administration of the anti-TNF- ⁇ antibody of the disclosure can precede or follow administration of the combination therapeutic agent.
  • the anti-TNF- ⁇ antibody of the disclosure and combination therapeutic agent can be administered concurrently for a period of time, followed by a second period of time in which the administration of the anti-TNF- ⁇ antibody of the disclosure and the combination therapeutic agent is alternated.
  • such agents can be administered in amounts that, if one or both of the agents is administered alone, is/are not therapeutically effective.
  • the combination therapeutic agent is an anti-rheumatic drug, an anti-inflammatory agent, a chemotherapeutic agent, a radiotherapeutic, an immunosuppressive agent, or a cytotoxic drug.
  • Anti-rheumatic drugs include, but are not limited to, auranofm, azathioprine, chloroquine, D-penicillamine, gold sodium thiomalate hydroxychloroquine, Myocrisin and sulfasalzine methotrexate.
  • Anti-inflammatory agents include, but are not limited to, dexamethasone, pentasa, mesalazine, asacol, codeine phosphate, benorylate, fenbufen, naprosyn, diclofenac, etodolac and indomethacin, aspirin and ibuprofen.
  • Chemotherapeutic agents include, but are not limited to, radioactive molecules, toxins, also referred to as cytotoxins or cytotoxic agents, which includes any agent that is detrimental to the viability of cells, agents, and liposomes or other vesicles containing chemotherapeutic compounds.
  • chemotherapeutic agents include but are not limited to 1-dehydrotestosterone, 5-fluorouracil decarbazine, 6-mercaptopurine, 6- thioguanine, actinomycin D, adriamycin, aldesleukin, alkylating agents, allopurinol sodium, altretamine, amifostine, anastrozole, anthramycin (AMC)), anti-mitotic agents, cisdichlorodiamine platinum (II) (DDP) cisplatin), diamino dichloro platinum, anthracyclines, antibiotics, antimetabolites, asparaginase, BCG live (intravesical), betamethasone sodium phosphate and betamethasone acetate, bicalutamide, bleomycin sulfate, busulfan, calcium leucouorin, calicheamicin, capecitabine, carboplatin, lomustine (CCNU), carmustine (BSNU), Chloramb
  • the combination therapeutic agent is a TNF- ⁇ antagonist other than the anti-TNF- ⁇ antibody of the disclosure.
  • TNF- ⁇ antagonists include, but are not limited to, soluble TNF- ⁇ receptors; etanercept (ENBRELTM; Immunex) or a fragment, derivative or analog thereof; infliximab (REMICADE®; Centacor) or a derivative, analog or antigen-binding fragment thereof; IL-IO, which is known to block TNF- ⁇ production via interferon- ⁇ -activated macrophages (Oswald et al, 1992, Proc. Natl. Acad. Sci.
  • the present disclosure provides therapeutic regimens involving the administration of the anti-TNF- ⁇ antibodies of the disclosure.
  • the therapeutic regimen will vary depending on the patient's age, weight, and disease condition.
  • the therapeutic regimen can continue for 2 weeks to indefinitely. In specific embodiments, the therapeutic regimen is continued for 2 weeks to 6 months, from 3 months to 5 years, from 6 months to 1 or 2 years, from 8 months to 18 months, or the like.
  • the therapeutic regimen can be a non-variable dose regimen or a multiple-variable dose regimen, for example as described in WO 2005/110452, which is incorporated by reference in its entirety.
  • the anti-TNF- ⁇ antibody can be administered as a sterile, preservative-free solution for subcutaneous administration.
  • the drug product is supplied as either a single-use, prefilled pen within which is enclosed a 1 mL prefilled glass syringe, or as a single-dose, 1 mL prefilled glass syringe.
  • the syringe delivers 0.8 mL of a pharmaceutically acceptable solution comprising the anti-TNF- ⁇ antibody of the disclosure.
  • the solution contains 4.93 mg sodium chloride, 0.69 mg monobasic sodium phosphate dihydrate, 1.22 mg dibasic sodium phosphate dihydrate, 0.24 mg sodium citrate, 1.04 mg citric acid monohydrate, 9.6 mg mannitol, 0.8 mg polysorbate 80, and water for injection (USP) with sodium hydroxide added as necessary to adjust pH.
  • USP water for injection
  • the syringe delivers 0.4 mL of a pharmaceutically acceptable solution comprising the anti-TNF- ⁇ antibody of the disclosure.
  • the solution contains 2.47 mg sodium chloride, 0.34 mg monobasic sodium phosphate dihydrate, 0.61 mg dibasic sodium phosphate dihydrate, 0.12 mg sodium citrate, 0.52 mg citric acid monohydrate, 4.8 mg mannitol, 0.4 mg polysorbate 80, and water for injection (USP) with sodium hydroxide added as necessary to adjust pH.
  • USP water for injection
  • an anti-TNF- ⁇ antibody of the disclosure can be administered at a dose of 10 to 50 mg (e.g., 10 mg, 15 mg, 20 mg, 25 mg, 30 mg, 35 mg, 40 mg, 45 mg or 50 mg) every other week.
  • Methotrexate, glucocorticoids, salicylates, nonsteroidal anti-inflammatory drugs (NSAIDs), analgesics or other disease-modifying antirheumatics drug (DMARDs) can be continued during treatment with the anti-TNF- ⁇ antibody of the disclosure.
  • NSAIDs nonsteroidal anti-inflammatory drugs
  • DMARDs disease-modifying antirheumatics drug
  • some patients not taking concomitant methotrexate can derive additional benefit from increasing the dosing frequency from biweekly to weekly.
  • an anti-TNF- ⁇ antibody of the disclosure is administered at a dose that depends on the patient's weight.
  • the dose for pediatric patients weighing 15 kg (33 lbs) to under 30 kg (66 lbs) ranges from 5 to 25 mg (e.g., 5 mg, 7.5 mg, 10 mg, 12.5 mg, 15 mg, 20 mg, or 25 mg) every other week.
  • the dose for pediatric patients weighing greater than 30 kg (66 lbs) ranges fromlO to 50 mg (e.g., 10 mg, 15 mg, 20 mg, 25 mg, 30 mg, 35 mg, 40 mg, 45 mg or 50 mg) every other week.
  • Methotrexate, glucocorticoids, salicylates, NSAIDs or analgesics can be continued during treatment with the anti-TNF- ⁇ antibody.
  • an anti-TNF- ⁇ antibody of the disclosure can be administered in certain non- limiting embodiments at a dose of 40-280 mg (e.g., 40 mg, 80 mg, 100 mg, 120 mg, 140 mg, 160 mg, 180 mg, 200 mg, 240 mg, or 280 mg) given initially (on Day 1 or divided between Day 1 and Day T), followed by a dose of approximately 40% to 60% (e.g., 50%) of the initial dose two weeks later (Day 15). Two weeks later (Day 29), a maintenance dose of 20% to 30% (e.g., 25%) of the initial dose is administered every other week.
  • Aminosalicylates, corticosteroids, and/or immunomodulatory agents e.g.
  • an anti-TNF- ⁇ antibody of the disclosure can be administered in certain non- limiting embodiments at a dose of 40-160 mg (e.g., 40 mg, 80 mg, 100 mg, 120 mg, 140 mg, or 160 mg given initially followed by half the initial dose given every other week starting one week after the initial dose.
  • kits containing the anti-TNF- ⁇ antibodies (including antibody conjugates) of the disclosure are pharmaceutical kits containing the anti-TNF- ⁇ antibodies (including antibody conjugates) of the disclosure.
  • the pharmaceutical kit is a package comprising the anti-TNF- ⁇ antibody of the disclosure (e.g., either in lyophilized form or as an aqueous solution) and one or more of the following:
  • a combination therapeutic agent for example as described in Section 7.10 above;
  • a device for administering the anti-TNF- ⁇ antibody for example a pen, needle and/or syringe
  • each unit dose of the anti-TNF- ⁇ antibody is packaged separately, and a kit can contain one or more unit doses (e.g., two unit doses, three unit doses, four unit doses, five unit doses, eight unit doses, ten unit doses, or more).
  • the one or more unit doses are each housed in a syringe or pen.
  • the diagnostic kit is a package comprising the anti-TNF- ⁇ antibody of the disclosure (e.g., either in lyophilized form or as an aqueous solution) and one or more reagents useful for performing a diagnostic assay.
  • the kit can include substrates and cofactors required by the enzyme (e.g., a substrate precursor which provides the detectable chromophore or fluorophore).
  • substrates and cofactors required by the enzyme e.g., a substrate precursor which provides the detectable chromophore or fluorophore.
  • other additives can be included, such as stabilizers, buffers (e.g., a block buffer or lysis buffer), and the like.
  • the anti-TNF- ⁇ antibody included in a diagnostic kit is immobilized on a solid surface, or a solid surface (e.g. , a slide) on which the antibody can be immobilized is included in the kit.
  • the relative amounts of the various reagents can be varied widely to provide for concentrations in solution of the reagents which substantially optimize the sensitivity of the assay.
  • the antibody and one or more reagents can be provided (individually or combined) as dry powders, usually lyophilized, including excipients which on dissolution will provide a reagent solution having the appropriate concentration.
  • Peptides were synthesized using a multi-pin format by Mimotopes (Adelaide, Australia). The sequences of the D2E7 light and heavy chain V regions were synthesized as 15-mer peptides overlapping by 12 amino acids ( Figure 1 and Table 1) for a total of 69 peptides. Peptides arrived lyophilized and were re-suspended in DMSO (Sigma-Aldrich) at approximately 1-2 mg/mL. Stock peptides were kept frozen at -2O 0 C.
  • T75 culture flasks (Costar) were seeded with 10 8 freshly isolated PBMC in a total volume of 30 mL AIM V media (Invitrogen). Excess PBMC were frozen at -8O 0 C in 90% fetal calf serum (FCS), 10% DMSO at 5 x 10 7 cells/ml. T75 flasks were incubated at 37 0 C in 5% CO 2 for 2 hours. Nonadherent cells were removed, and the adherent monolayer was washed with DPBS.
  • FCS fetal calf serum
  • AIM V media containing 800 units/mL of GM- CSF (R and D Systems) and 500 units/mL IL-4 (R and D Systems) were added. Flasks were incubated for 5 days. On day 5 IL- l ⁇ (Endogen) and TNF- ⁇ (Endogen) were added to 50 pg/mL and 0.2 ng/ml. Flasks were incubated for two more days.
  • dendritic cells were collected by the addition of 3 mL of 100 mM EDTA containing 0.5 to 1.0 mg Mitomycin C (Sigma- Aldrich) for a final concentration of 10 mM EDTA and 16.5 to 33 ⁇ g/mL Mitomycin C.
  • dendritic cells can be irradiated with 4,000 rads for fixation. Flasks were incubated an additional hour at 37 0 C and 5% CO 2 . Dendritic cells were collected, and washed in AIM V media 2-3 times.
  • Positive control wells contained DMSO at 0.25% and tetanus toxoid (List Biologicals or CalBioChem) at 1 ⁇ g/mL. Cultures were incubated for 5 days. On day 5, 0.25 ⁇ Ci per well of tritiated thymidine (Amersham or GE Healthcare) was added. Cultures were harvested on day 6 to f ⁇ ltermats using a Packard Filtermate Cell harvester. Scintillation counting was performed using a Wallac MicroBeta 1450 scintillation counter (Perkin Elmer).
  • Average background CPM values were calculated by averaging individual results from 6 to 12 replicates. The CPM values of the four positive control wells were averaged. Replicate or triplicate wells for each peptide were averaged. Stimulation index values for the positive control and the peptide wells were calculated by dividing the average experimental CPM values by the average control values. In order to be included in the dataset, a stimulation index of greater than 3.0 in the tetanus toxoid positive control wells was required. A response was noted for any peptide resulting in a stimulation index of 2.95 or greater. Peptides were tested using peripheral blood samples from a group of 81 donors. Responses to all peptides were compiled. For each peptide tested, the percentage of the donor set that responded with a stimulation index of 2.95 or greater was calculated. In addition, the average stimulation index for all donors was calculated.
  • HLA DRBl and HLA DQBl alleles were determined for each donor using the commercially available Dynal RELI typing kits (Invitrogen, UK). Low stringency SSO results are reported. HLA associations were determined for responsiveness to any given peptide using a Chi-squared analysis (one degree of freedom). Where an allele was present in both of the responder and non-responder populations, a relative risk value was reported.
  • TNF- ⁇ was adhered onto a microwell plate, by contacting the plate with a solution of TNF- ⁇ at a concentration of 1 ⁇ g/mL in PBS over night at 4°C. The plate was washed in 0.1% Tween 20 in PBS and blocked in Superblock (Thermo Scientific, Rockford, IL).
  • Binding affinities of anti-TNF- ⁇ antibodies were measured by using a BIAcore 2000 and 3000 surface plasmon resonance system (BIAcore, GE Healthcare, Piscataway, NJ). Polyclonal goat anti-human Fc antibody (Jackson Immunoresearch) was first immobilized to the biosensor surface using standard BIAcore amine coupling reagents (N-ethyl-N'-dimethylamino-propylcarbodiimide, EDC; N-hydroxysuccinimide, NHS; and ethanolamine HCl, pH 8.5), followed by the capture of anti-TNF- ⁇ antibodies (D2E7 and D2E7 variants) on parallel surfaces at a low flow rate of 5 ⁇ L/min.
  • TNF- ⁇ was injected to all flow cells at a flow rate of 80 ⁇ L/min for three minutes to monitor association followed by a 30- minute flow of HBS-P running buffer (10 mM HEPES, 150 mM sodium chloride, 0.005% P-20, pH 7.4) to monitor the dissociation phase.
  • HBS-P running buffer 10 mM HEPES, 150 mM sodium chloride, 0.005% P-20, pH 7.4
  • TNF- ⁇ R&D systems, Minneapolis, MN
  • the surface was regenerated with 1.5% H3PO4 at a flow rate of 100 ⁇ L/min in two brief pulses at the end of each cycle.
  • the binding kinetics of each TNF- ⁇ and antibody pair were calculated from a global analysis of sensorgram data collected from the different concentrations of TNF- ⁇ using the BIAevaluate program. Double referencing was applied in each analysis to eliminate background responses from the reference surface and buffer only control (0 nM of TNF- ⁇ ).
  • the dissociation constants (K D ), the association rate constants (Ic 0n ) and the dissociation rate constants (k o ff) of each binding pair was obtained by simultaneously fitting the association and dissociation phases of the sensorgram using the 1 : 1 Langmuir binding with mass transfer model. Each set of experiments was performed 3 separate times.
  • CD4+ T cell epitope peptides were identified by an analysis of the percent responses to the peptides within the set of 81 donors. The average percent response and standard deviation were calculated for all peptides tested describing the D2E7 heavy chain and light chain. A response rate greater than or equal to the average background response plus three standard deviations was considered a potential CD4+ T cell epitope.
  • For the D2E7 light chain V region 32 peptides were tested (Figure 2) which resulted in an average background percent response of 5.09 + 3.53%. Three standard deviations above background was determined to be 15.68%.
  • One peptide at position 8 displayed this level of response in the D2E7 light chain peptide dataset, with a response rate of 17.28% ( Figure X).
  • the average stimulation index was calculated for all peptides in the dataset.
  • Light chain peptide #8 had a high average stimulation index of 1.97 + 0.08 s.e.m.
  • the peptide at position #11 returned an average stimulation index of 1.63 + 0.32 s.e.m.
  • Peptide #27 in the light chain dataset had an average SI of 1.83. This is due to a single donor with an unusually high stimulation index of 29 to this peptide.
  • Heavy chain peptide #20 had an average stimulation index value of 1.34 + 0.05 s.e.m. All of these values are significantly higher than the average stimulation index for all peptides in the two datasets (1.02 + 0.02 for all 68 heavy chain and light chain peptides).
  • HLA class II genotypes of all 81 donors in the peptide dataset were determined using a low-stringency SSO PCR-based method. Associations between the presence of a particular HLA allele and responses to the two VL peptides were determined by chi squared analysis. Fischer P values and relative risks were determined for all HLA types and both peptides (Table 3). There were no significant correlations between any HLA DR or DQ type and a response to VL peptide #8 (T22-Y36). This result suggests that the peptide is capable of binding to HLA class II molecules in a broadly promiscuous manner.
  • HLA-DR3 is in linkage disequilibrium with HLA-DQ2
  • the HLA responses to the VH peptide #20 were not tested as there were too few total responders. Since the responders to the two VL peptides were discrete it can be concluded that they represent two separate peptide epitopes. Therefore, the D2E7 VH and VL region contains three prominent peptide epitope regions.
  • Alanine scan modifications A twenty-one amino acid sequence of the D2E7 light chain encompasses the epitopes at T22-Y36 and N31-K45. The twenty one amino acid sequence selected was C23-K45. Alanine modifications were incorporated at each amino acid (Table 4). A set of 99 donors was tested with the variant peptides ( Figure 4). The parent 21 -mer was created 4 times within the peptide set. These four replicates serve as a control for the reproducibility of the assay. The average parent peptide response was 8.3%, with a CV% of 30%. Therefore, variant peptides with an average percent of less than 5.8% could be considered to have a reduced rate of response.
  • the most reduced variants were C23A (2.02%) and P40A (3.03%, see Figure 4).
  • the cysteine at position 23 is invariant, and is therefore not a good candidate for modification in the whole protein. Due to the unique nature of pro line residues a modification of this residue is also not likely to yield a functional variant antibody.
  • the third candidate would be Y32A (4.04%). Additionally, there are a number of variants that resulted in an average response rate of 5.05%. These changes could also be effective but would need to be tested as whole protein molecules for both reduced immunogenicity and functional activity.
  • the double modifications contained a glutamine or a glycine at position 32, or a serine or glycine at position 34.
  • a total of 79 peptides were tested including two syntheses of the parent 21-mer peptide.
  • a total of 102 donors were tested with the variant peptides and the results are shown in Figure 5.
  • the average percent response of the parent peptides was 10.3 + 2.1%. For a percent response rate to be less than 3 standard deviations from the parent the response rate would be less than 4%.
  • the average stimulation index for the parent peptides was 1.49 + 0.15. For a stimulation index to reach three standard deviations below the parent response it would be 1.03 or lower.
  • a TNF- ⁇ toxicity bioassay was performed. L292 cells were seeded into 96 well plates, and a constant concentration of TNF- ⁇ was added to the culture medium. The variant antibodies were titrated into the medium. An EC 50 value was determined for each variant (Table 9). Similarly, the variant Q27R + A34S displayed an EC50 value approximately equivalent to the parent D2E7 antibody.
  • the D2E7 antibody was subjected to comprehensive mutational analysis to identify mutants that had increased affinity to TNF- ⁇ as compared to D2E7.
  • the increased affinity of candidate mutants to TNF- ⁇ was analyzed by ELISA and BIAcore to confirm their characteristics as compared to D2E7.

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